# reads aligned to multi-references **URL:** \ **Category:** Uncategorized\ **Created:** [June 2, 2023, 8:14am UTC](https://help.galaxyproject.org/t/reads-aligned-to-multi-references/10164 "2023-06-02T08:14:48Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![huiping](https://avatars.discourse-cdn.com/v4/letter/h/9f8e36/32.png) [@huiping](https://help.galaxyproject.org/u/huiping)\ **Post date:** [June 2, 2023, 8:14am UTC](https://help.galaxyproject.org/t/reads-aligned-to-multi-references/10164/1 "2023-06-02T08:14:49Z")
Below is the result from bowtie2 aligner using multi-fasta references. I wonder what the number in column 4 means? Thanks. |1b\_EU781828|9359|160810|84317| |1b\_EU781827|9413|103840|48024| |1b\_D90208|9413|37970|19835| |1b\_M58335|9416|36799|19551| |1e\_KC248194|9422|4518|2222| |1l\_KC248197|9433|2819|731| |1d\_KJ439768|9451|2271|1190| |1a\_AF009606|9646|911|381| |2m\_JF735111|9618|370|158| |1a\_M62321|9401|187|61| |1a\_EF407457|9286|168|64| |1l\_KC248196|9428|13|3| |1a\_HQ850279|9191|10|5| |2k\_AB031663|9488|10|0| |1a\_AJ278830|9610|8|3| |3i\_FJ407092|9433|8|2| |1n\_KJ439781|9447|6|3| |2k\_JX227953|9380|6|1| |1a\_M67463|9416|5|3| |1i\_KJ439772|9421|5|2| |2j\_HM777358|9112|2|1| |2a\_D00944|9589|1|1| |2u\_JF735112|9520|1|0| |3a\_D28917|9454|1|1| |3e\_KJ470618|9458|1|0| |3i\_JX227955|9350|1|0| |4c\_FJ462436|9468|1|1| |6xe\_JX183557|9460|1|1| |\*|0|0|650418| |1c\_AY051292|9440|0|0| |1c\_AY651061|9441|0|0| |1c\_D14853|9487|0|0| |1g\_AM910652|9490|0|0| |1h\_KC248198|9421|0|0| |1h\_KC248199|9420|0|0| |1j\_KJ439773|9413|0|0| |1k\_KJ439774|9446|0|0| |1l\_KC248193|9430|0|0| |1m\_KJ439778|9448|0|0| |1m\_KJ439782|9448|0|0| |1n\_KJ439775|9411|0|0| |1o\_KJ439779|9413|0|0| |1o\_MH885469|9359|0|0| |2a\_AB047639|9678|0|0| |2a\_HQ639944|9392|0|0| |2b\_AB030907|9654|0|0| |2b\_AB661382|9102|0|0| |2b\_AB661388|9102|0|0| |2b\_D10988|9511|0|0| |2c\_D50409|9513|0|0| |2c\_JX227949|9295|0|0| |2d\_JF735114|9508|0|0| |2e\_JF735120|9825|0|0| |2f\_KC844042|9472|0|0| |2f\_KC844050|9470|0|0| |2i\_DQ155561|9370|0|0| |2j\_HM777359|9383|0|0| |2j\_JF735113|9509|0|0| |2m\_JX227967|9383|0|0| |2q\_F666428|9566|0|0| |2q\_F666429|9398|0|0| |2r\_JF735115|9512|0|0| |2t\_KC197238|9616|0|0| |2v\_MW041295|9403|0|0| |2v\_MW041297|9464|0|0| |2v\_MW041298|9419|0|0| |2v\_MW041299|9472|0|0| |3a\_D17763|9456|0|0| |3a\_J714194|9429|0|0| |3a\_X76918|9390|0|0| |3b\_D49374|9444|0|0| |3b\_JQ065709|9383|0|0| |3d\_KJ470619|9458|0|0| |3g\_JF735123|9634|0|0| |3g\_JX227954|9353|0|0| |3h\_JF735121|9579|0|0| |3h\_JF735126|9633|0|0| |3k\_D63821|9450|0|0| |3k\_JF735122|9660|0|0| |4a\_DQ418789|9295|0|0| |4a\_DQ988074|9054|0|0| |4a\_Y11604|9354|0|0| |4b\_FJ462435|9440|0|0| |4d\_DQ418786|9273|0|0| |4d\_EU392172|9299|0|0| |4d\_FJ462437|9088|0|0| |4f\_EF589161|9304|0|0| |4f\_EU392174|9298|0|0| |4f\_EU392175|9297|0|0| |4g\_FJ462432|9435|0|0| |4g\_JX227963|9314|0|0| |4g\_JX227971|9174|0|0| |4k\_EU392171|9281|0|0| |4k\_EU392173|9312|0|0| |4k\_FJ462438|9438|0|0| |4l\_FJ839870|9388|0|0| |4l\_JX227957|9317|0|0| |4m\_FJ462433|9425|0|0| |4m\_JX227972|9305|0|0| |4n\_FJ462441|9435|0|0| |4n\_JX227970|9301|0|0| |4o\_FJ462440|9422|0|0| |4o\_JX227977|9286|0|0| |4p\_FJ462431|9475|0|0| |4q\_FJ462434|9433|0|0| |4r\_FJ462439|9440|0|0| |4r\_JX227976|9319|0|0| |4s\_JF735136|9426|0|0| |4t\_FJ839869|9488|0|0| |4v\_HQ537008|9174|0|0| |4v\_HQ537009|9177|0|0| |4v\_JX227959|9323|0|0| |4v\_JX227960|9270|0|0| |4w\_FJ025855|9242|0|0| |4w\_FJ025856|9271|0|0| |5a\_AF064490|9408|0|0| |5a\_Y13184|9343|0|0| |6a\_AY859526|9355|0|0| |6a\_EU246930|9376|0|0| |6a\_HQ639936|9315|0|0| |6a\_Y12083|9340|0|0| |6b\_D84262|9628|0|0| |6c\_EF424629|9459|0|0| |6d\_D84263|9615|0|0| |6e\_DQ314805|9468|0|0| |6e\_EU246932|9382|0|0| |6f\_DQ835760|9454|0|0| |6f\_EU246936|9370|0|0| |6g\_D63822|9461|0|0| |6g\_DQ314806|9462|0|0| |6h\_D84265|9621|0|0| |6i\_DQ835762|9458|0|0| |6i\_DQ835770|9447|0|0| |6j\_DQ835761|9442|0|0| |6j\_DQ835769|9454|0|0| |6k\_D84264|9601|0|0| |6l\_EF424628|9453|0|0| |6l\_JX183556|9413|0|0| |6m\_DQ835766|9449|0|0| |6m\_DQ835767|9444|0|0| |6n\_DQ278894|9441|0|0| |6n\_DQ835768|9447|0|0| |6n\_EU246938|9361|0|0| |6o\_EF424627|9450|0|0| |6o\_EU246934|9364|0|0| |6p\_EF424626|9453|0|0| |6q\_EF424625|9463|0|0| |6r\_EU408328|9449|0|0| |6s\_EU408329|9473|0|0| |6t\_EF632071|9406|0|0| |6t\_EU246939|9364|0|0| |6u\_EU246940|9367|0|0| |6v\_EU158186|9428|0|0| |6v\_EU798760|9461|0|0| |6v\_EU798761|9429|0|0| |6w\_DQ278892|9448|0|0| |6w\_EU643834|9147|0|0| |6w\_EU643836|9144|0|0| |6xa\_EU408330|9451|0|0| |6xa\_EU408331|9470|0|0| |6xa\_EU408332|9443|0|0| |6xb\_JX183552|9533|0|0| |6xb\_KJ567645|9401|0|0| |6xc\_KJ567651|9442|0|0| |6xd\_KM252789|9432|0|0| |6xd\_KM252790|9435|0|0| |6xd\_KM252791|9434|0|0| |6xe\_KM252792|9401|0|0| |6xf\_KJ567646|9428|0|0| |6xf\_KJ567647|9421|0|0| |6xg\_MH492360|9318|0|0| |6xg\_MH492361|9318|0|0| |6xg\_MH492362|9318|0|0| |6xh\_MG879000|9057|0|0| |6xi\_JX183549|9448|0|0| |6xi\_MZ504973|9361|0|0| |6xi\_MZ504976|9361|0|0| |6xj\_DQ278891|9440|0|0| |6xj\_DQ278893|9430|0|0| |6xj\_MZ171127|9393|0|0| |6xj\_MZ171134|9396|0|0| |7a\_EF108306|9357|0|0| |7b\_KX092342|9382|0|0| |8a\_MH590698|9347|0|0| |8a\_MH590699|9351|0|0| |8a\_MH590700|9547|0|0| |8a\_MH590701|9437|0|0| ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [June 2, 2023, 4:12pm UTC](https://help.galaxyproject.org/t/reads-aligned-to-multi-references/10164/2 "2023-06-02T16:12:24Z")
Duplicated post, see [Mapping reads to references by PEAR, bowtie2, samtool idx and sort tools - #4 by huiping](https://help.galaxyproject.org/t/mapping-reads-to-references-by-pear-bowtie2-samtool-idx-and-sort-tools/10156/4) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [June 2, 2023, 4:12pm UTC](https://help.galaxyproject.org/t/reads-aligned-to-multi-references/10164/3 "2023-06-02T16:12:30Z")