Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A14 F56 I20 R2 1958 92.1 3575798 91.1% 3257551 126.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 2,198,491 A→G N164N (AAT→AAC)  U712_11015 ← Chemotaxis protein methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068812,198,4910AG100.0% 158.6 / NA 50N164N (AAT→AAC) U712_11015Chemotaxis protein methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (25/25);  total (25/25)

TCTGTAAAATAAATAAATACATTGCGGCACACAATTAAGTCAAAGTCTTGTTCATAACGATCAGCCAGTAGATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGCTTTTACTTCATAACTTCTATTTGCATTTTGAGTAAAATAACGATCCTTCACAGATGAAGGTACTTCCTGTAAAGACCTCTCCTGATAGACGCCTTTTTTCGCTTTCTCCAATGCTTTTTCATCAATATCAGTCGCCAGGATCTGAAAGCCGGGAAGAC  >  CP006881/2198357‑2198624
                                                                                                                                      |                                                                                                                                     
tCTGTAAAATAAATAAATACATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGtttt                                                                                                                                   >  3:337826/1‑139 (MQ=255)
           aataaataCATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATaa                                                                                                                        <  3:71972/139‑1 (MQ=255)
           aataaataCATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATaa                                                                                                                        <  6:223715/139‑1 (MQ=255)
             taaataCATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACg                                                                                                                      <  7:346063/139‑1 (MQ=255)
               aataCATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGAt                                                                                                                    <  4:305137/139‑1 (MQ=255)
               aataCATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGAt                                                                                                                    <  8:137227/139‑1 (MQ=255)
                   cATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGCTCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCttt                                                                                                                >  8:103588/1‑139 (MQ=255)
                   cATTGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCttt                                                                                                                <  2:60363/139‑1 (MQ=255)
                      tGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTca                                                                                                              >  5:71533/1‑138 (MQ=255)
                      tGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTca                                                                                                              >  3:60538/1‑138 (MQ=255)
                      tGCGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTca                                                                                                              >  8:169309/1‑138 (MQ=255)
                      tGCGGCACACGATTAAGTCAAAGGCTTGTTCATAACGATCCGCCAGCAAATTGTGATTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTca                                                                                                              >  4:72123/1‑138 (MQ=255)
                        cGGCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTca                                                                                                              >  3:98203/1‑136 (MQ=255)
                         ggCACACGATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGa                                                                                                          <  4:337826/139‑1 (MQ=255)
                           cacacgATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATAGTGCTTTTTCAATGTATTATTCTTTTTGATTTCCGTTTTCACTTCATACCTACTATTTGCGTTTTGCG‑AAAATAACGATCTTTCACAGAtag                                                                                                       >  3:276149/1‑137 (MQ=255)
                             cacgATTAAGTCAAAGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGAtagc                                                                                                      >  6:25971/1‑136 (MQ=255)
                                          aaGTCTTGTTCATAACGATCCGCCAGCAATTTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTATTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTga                                                                                          >  1:365270/1‑137 (MQ=255)
                                          aaGTCTTGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGCTCTTTCACAGATAGCGGCCCTTCCTGt                                                                                          >  5:282011/1‑138 (MQ=255)
                                                tGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGAcc                                                                                   >  3:65381/1‑139 (MQ=255)
                                                tGTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGAcc                                                                                   >  8:4063/1‑139 (MQ=255)
                                                 gTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGAtagcgg                                                                                                    >  4:98381/1‑116 (MQ=255)
                                                 gTTCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGAtagcgg                                                                                                    <  3:98381/121‑6 (MQ=255)
                                                  ttCATAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCAATTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGAccg                                                                                  <  7:405160/138‑2 (MQ=255)
                                                      tAACGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCt                                                                             >  1:321569/1‑139 (MQ=255)
                                                       aaCGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCTTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACAGCTCCt                                                                             >  8:372215/1‑138 (MQ=255)
                                                       aaCGATCCGCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCt                                                                             >  4:296291/1‑138 (MQ=255)
                                                            tccgCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGAta                                                                                                        <  6:134718/103‑2 (MQ=255)
                                                            tccgCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGAta                                                                                                        >  5:134718/4‑105 (MQ=255)
                                                            tccgCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCTCTTCCTGTAAAGACCGCTCCTGATaaa                                                                       >  2:168428/4‑137 (MQ=255)
                                                            tccgCCAGCAAATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATaaa                                                                       >  5:89194/4‑137 (MQ=255)
                                                                           tgCTTTTTGAATGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCt                                                         <  2:133478/138‑1 (MQ=255)
                                                                                     aTGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCt                                                         >  8:217974/1‑128 (MQ=255)
                                                                                     aTGTAATATTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCt                                                         <  7:217974/128‑1 (MQ=255)
                                                                                          atatTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCttttt                                         <  2:151721/139‑1 (MQ=255)
                                                                                          atatTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCttttt                                         <  6:254012/139‑1 (MQ=255)
                                                                                          atatTCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCtttt                                          <  4:376529/138‑1 (MQ=255)
                                                                                             ttCTTTTTGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTtcat                                      <  6:89194/139‑1 (MQ=255)
                                                                                                  tttGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGa                                                                                                          <  1:212086/66‑1 (MQ=255)
                                                                                                  tttGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGa                                                                                                          <  3:39126/66‑1 (MQ=255)
                                                                                                  tttGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGa                                                                                                          >  4:39126/1‑66 (MQ=255)
                                                                                                  tttGATTTCCGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGa                                                                                                          >  2:212086/1‑66 (MQ=255)
                                                                                                          ccGTTTTCACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGc                         >  4:331592/1‑139 (MQ=255)
                                                                                                           cgttttcACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGc                         <  3:57383/135‑1 (MQ=255)
                                                                                                            gttttcACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGcta                       <  5:25971/137‑3 (MQ=255)
                                                                                                            gttttcACTTCATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGcta                       <  7:103588/137‑3 (MQ=255)
                                                                                                                      cATAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGa               <  3:331592/137‑1 (MQ=255)
                                                                                                                       aTAACTTCTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAg            <  7:254042/139‑1 (MQ=255)
                                                                                                                       aTAACTTCTATTTGCGTTATGCGTAATATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAATACCGCTCCTGATAATCGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAg            <  2:365270/139‑1 (MQ=255)
                                                                                                                              cTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGata             <  4:315547/131‑3 (MQ=255)
                                                                                                                              cTATTTGCGTTTTGCGTAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGata             >  3:315547/1‑129 (MQ=255)
                                                                                                                                 tttgcgttttgcgtAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAGCCCGGaa     <  6:19195/136‑1 (MQ=255)
                                                                                                                                 tttgcgttttgcgtAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAGCCCGGaa     <  3:296291/136‑1 (MQ=255)
                                                                                                                                 tttgcgttttgcgtAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAGCCCGGaa     <  1:347301/136‑1 (MQ=255)
                                                                                                                                 tttgcgttttgcgtAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAGCCCGGaa     <  5:68061/136‑1 (MQ=255)
                                                                                                                                 tttgcgttttgcgtAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAGCCCGGaa     <  5:380305/136‑1 (MQ=255)
                                                                                                                                 tttgcgttttgcgtAAAATAACGATCTTTCACAGATAGCGGCACTTCCTGTAAAGACCGCTCCTGATAAACGCCTTTTTTCGCTTTTTCCAATGCTTTTTCATCAATATCCGTCGCTAAAATCTGATAGCCCGGAAGAc  >  2:51100/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                     
TCTGTAAAATAAATAAATACATTGCGGCACACAATTAAGTCAAAGTCTTGTTCATAACGATCAGCCAGTAGATTGTGCTTTTTGAATGTAATATTCTTTTTGATTTCCGCTTTTACTTCATAACTTCTATTTGCATTTTGAGTAAAATAACGATCCTTCACAGATGAAGGTACTTCCTGTAAAGACCTCTCCTGATAGACGCCTTTTTTCGCTTTCTCCAATGCTTTTTCATCAATATCAGTCGCCAGGATCTGAAAGCCGGGAAGAC  >  CP006881/2198357‑2198624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A