Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	804,673	A→T	L135I (TTA→ATA)	dtpT ←	Di‑/tripeptide transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	804,673	0	A	T	100.0%	188.9 / NA	66	L135I (TTA→ATA)	dtpT	Di‑/tripeptide transporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (29/37);  total (29/37)

AGTGTTGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTAAACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAATTCTGTCA  >  USA300TCH1516_ALE/804538‑804809                                                                                                                                        |                                                                                                                                         aGTGTTGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCt                                                                                                                                      >  2:272472/1‑140 (MQ=255) aGTGTTGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCt                                                                                                                                      >  2:509915/1‑140 (MQ=255)      tGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGACACCCATGCGTGAAATGTTTGGCTTCATTATACCTGAAcc                                                                                                                                 >  2:207655/1‑140 (MQ=255)         aaaaTAATAGGTGATAATAAAGCACCCATATCAACTGACATAAAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCaat                                                                                                                              <  1:20426/140‑1 (MQ=255)                taGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACAATATTTGAAATGTTTGGCTTCATTATTCCTGACCCACTAatgttg                                                                                                                       >  1:438113/1‑140 (MQ=255)                       taataaTGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACa                                                                                                                <  1:689947/140‑1 (MQ=255)                       taataaTGCACCCAAATTAACTAACAAATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACa                                                                                                                <  1:568928/140‑1 (MQ=255)                        aataatGTCCCCATATTAACTGACATATAAAAAATAACAAAACCTGCATCCAGACGGCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACAt                                                                                                               <  1:301764/140‑1 (MQ=255)                        aataatGCACCCATATTAACGAACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGGTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACAt                                                                                                               <  1:581460/140‑1 (MQ=255)                           aatGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTTAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTGTATTATACCTGAACCACTAATGATGAGGAACAttaa                                                                                                            >  2:844494/1‑138 (MQ=255)                             tGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGAtg                                                                                                          >  2:466578/1‑140 (MQ=255)                              gCACCCAGATTAACTGACGTATAGAAAATAACAAAACCTTCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGAtgt                                                                                                         <  1:711400/140‑1 (MQ=255)                                   cATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATa                                                                                                    <  1:298959/140‑1 (MQ=255)                                   cATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATa                                                                                                    >  2:244158/1‑140 (MQ=255)                                    atatTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCATTAATGATGAAGAACATTGATGCGAATaa                                                                                                   >  2:779604/1‑140 (MQ=255)                                     tatTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAg                                                                                                  >  2:676620/1‑140 (MQ=255)                                     tatTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGGCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTAATTATACCTGTACCAATAATGAAGAAGAACATTGATGTGAAtcaa                                                                                                  >  1:691563/1‑137 (MQ=255)                                                    aGAATATAACATAGCCTGCTACCATACGTCTATCAAGTTCAGGATAGAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAAt                                                                                   <  1:16724/140‑1 (MQ=255)                                                       aaaTAACAAAACCTGCATCCATACGTCTATCATTTTTAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGt                                                                                <  2:442744/140‑1 (MQ=255)                                                       aaaTAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGAAAATGGt                                                                                >  2:263123/1‑140 (MQ=255)                                                       aaaTAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAAAGAAAAAGAACAACGAAGTGAATAAGCCGATCAATGCCACTgga                                                                                >  1:985005/1‑139 (MQ=255)                                                           aaCAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGc                                                                            <  2:896743/140‑1 (MQ=255)                                                           aaCAAAACCTGCATCCAGACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGc                                                                            <  1:49969/140‑1 (MQ=255)                                                            aCAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCCAATGGTAACCt                                                                           >  2:182127/1‑140 (MQ=255)                                                            aCAAAACCTGCATCCATACGTCTACCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAACt                                                                           >  2:758567/1‑140 (MQ=255)                                                               aaaCCTGTATCCATACGTCTATCATTTTCAGGAGATAAACGAAATAAATGCATAGAAATGTTTGGCTTCATAATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTaa                                                                        >  2:709495/1‑140 (MQ=255)                                                               aaaCCTGAATCCATACGTCTATCATTTTCAGGATATAAACGGCCTACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCGTaa                                                                        >  2:709457/1‑140 (MQ=255)                                                                         ccATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAACGGTATGCTTAAACAAATATGt                                                              <  1:514351/140‑1 (MQ=255)                                                                         ccAAACGTCTATCATTTTCAAGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAAAGGTAAGCTTAAACAAATATGt                                                              <  1:517068/140‑1 (MQ=255)                                                                           aTACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTcc                                                            <  1:143038/140‑1 (MQ=255)                                                                             aCGTCTATTATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGa                                                          <  1:244158/140‑1 (MQ=255)                                                                              cGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGat                                                         <  2:998246/140‑1 (MQ=255)                                                                              cGTCGACCATTTTCAGGATAGAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGTAAACGGTAAGCTTAAACAAATATGTCCGat                                                         <  1:287083/140‑1 (MQ=255)                                                                                 cTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGataat                                                      <  1:940242/140‑1 (MQ=255)                                                                                      aTTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGAtaataataa                                                 >  2:316016/1‑140 (MQ=255)                                                                                      aTTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACAAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGAtaataataa                                                 >  2:358348/1‑140 (MQ=255)                                                                                       ttttCAGGATATAAACCGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACAGTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATaaa                                                <  2:202879/140‑1 (MQ=255)                                                                                        tttcgtgATATAACGCGCCAACGATATTTGAAATGTTTGGCTTGATTATACCTGAACCAATAATGATGAAGAATATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAg                                               <  2:276009/134‑1 (MQ=255)                                                                                        tttCAGGATATAAAGGGCCAAGGATATTTGAAATGTTTGGCATCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAg                                               <  1:923056/140‑1 (MQ=255)                                                                                        tttCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAg                                               <  1:913474/140‑1 (MQ=255)                                                                                        tttCAGGATATAAACGGACAACGATATTTGAAATGTTTGGCTTCATTATACCTGAAACAATAAAGATGAAGAACATTGATGTGAATAAGCAGATTAATGCAAATGGTAAGCTTAAAAAAATAAGTCCGATAAAAATAAAg                                               >  2:952776/1‑140 (MQ=255)                                                                                          tCAGGATATAAACGGCCAAAGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGAc                                             <  1:794304/140‑1 (MQ=255)                                                                                           catgacataAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACt                                            <  2:955789/134‑1 (MQ=255)                                                                                           cAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACt                                            <  1:62965/140‑1 (MQ=255)                                                                                               atatAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGccc                                        >  2:190476/1‑138 (MQ=255)                                                                                                tataAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCAcc                                       >  2:400524/1‑140 (MQ=255)                                                                                                   aaaCGGCCAACGATATTTGAAATTTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCtaa                                    <  1:799788/140‑1 (MQ=255)                                                                                                     aCGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCtaata                                  <  2:14099/140‑1 (MQ=255)                                                                                                       ggCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGAAGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGAACGTAATaaa                                >  2:979437/1‑140 (MQ=255)                                                                                                        gcgacacatatTTGAATTGGTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAg                               <  2:197051/133‑1 (MQ=255)                                                                                                        gCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAg                               <  1:628043/140‑1 (MQ=255)                                                                                                        gCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAg                               <  1:529319/140‑1 (MQ=255)                                                                                                             cGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAgcg                          >  2:900592/1‑140 (MQ=255)                                                                                                             cGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGATAAGCTTAAACAAATATGTCAGAAAATACAAAAGACTACACCACATAAAggatca                          >  2:690186/1‑135 (MQ=255)                                                                                                             cGATATATGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAAAAATAAAGACTGCACCTAATAAAGTAgcg                          >  2:182824/1‑140 (MQ=255)                                                                                                              gATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAgcgc                         >  2:589091/1‑140 (MQ=255)                                                                                                                tctttGAAGTGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCct                       <  1:207655/138‑1 (MQ=255)                                                                                                                 atTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCctc                      <  1:466578/140‑1 (MQ=255)                                                                                                                   ttGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATACAGTAGCGCCTCTa                    >  2:508785/1‑140 (MQ=255)                                                                                                                   ttGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTa                    <  1:551800/140‑1 (MQ=255)                                                                                                                           tttGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGt            <  1:818698/140‑1 (MQ=255)                                                                                                                           gttggtgtCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGCTAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGt            <  2:639692/133‑1 (MQ=255)                                                                                                                            ttGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTa           >  1:716496/1‑140 (MQ=255)                                                                                                                             tgtgttCAGTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTaa          <  1:464482/136‑1 (MQ=255)                                                                                                                                    aTTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAATTCTGTc   >  1:152876/1‑140 (MQ=255)                                                                                                                                     ttATACCTGGACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAATTCTGTCa  <  1:255574/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                         AGTGTTGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTAAACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAATTCTGTCA  >  USA300TCH1516_ALE/804538‑804809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑