Hi, Jennifer,
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|