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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,229,564 C→T A277A (GCG→GCA)  hlyE ← hemolysin E

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,229,5640CT100.0% 194.2 / NA 59A277A (GCG→GCA) hlyEhemolysin E
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/27);  total (32/27)

TTTTTAAATGTGATAAACCTTATACCTTGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCCGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTGGCGGCATCGATAT  >  NC_000913/1229429‑1229691
                                                                                                                                       |                                                                                                                               
tttttAAATGTGATAAACCTTATACCTTGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGgctgct                                                                                                                              <  1:423862/139‑1 (MQ=255)
              taaCCTTATACCTTGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCaaaga                                                                                                                <  1:220205/138‑1 (MQ=255)
                    tataCCTTGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCAt                                                                                                          >  2:1058649/1‑139 (MQ=255)
                        ccTTGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTaaa                                                                                                      <  2:49643/139‑1 (MQ=255)
                           tGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCAt                                                                                                          <  2:1335922/132‑1 (MQ=255)
                           tGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCAt                                                                                                          >  1:1335922/1‑132 (MQ=255)
                             aGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAatcatc                                                                                                 <  1:1058649/139‑1 (MQ=255)
                                      agagaATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAatcat                                                                                                  <  2:485794/129‑1 (MQ=255)
                                      agagaATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAatcat                                                                                                  >  1:485794/1‑129 (MQ=255)
                                            taatCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGaa                                                                                  >  1:854180/1‑139 (MQ=255)
                                                        aGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAAt                                                                                 >  1:103034/1‑128 (MQ=255)
                                                        aGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAAt                                                                                 <  2:103034/128‑1 (MQ=255)
                                                                    ccTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGtttt                                                          >  1:1168214/1‑139 (MQ=255)
                                                                     cTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCa                                                                                          <  1:349483/106‑1 (MQ=255)
                                                                     cTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCa                                                                                          >  2:349483/1‑106 (MQ=255)
                                                                      tCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTgg                                                                             >  2:1059167/1‑118 (MQ=255)
                                                                      tCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTgg                                                                             <  1:1059167/118‑1 (MQ=255)
                                                                      tCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTa                                                        >  2:1089498/1‑139 (MQ=255)
                                                                       cAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTAt                                                       <  2:152680/139‑1 (MQ=255)
                                                                               gtCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGttt                                                                 <  1:1396539/121‑1 (MQ=255)
                                                                               gtCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGttt                                                                 >  2:1396539/1‑121 (MQ=255)
                                                                               gtCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTAtct                                                     >  1:714571/1‑133 (MQ=255)
                                                                               gtCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTAtct                                                     <  2:714571/133‑1 (MQ=255)
                                                                                          gtgtCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTaaa                                                                                                      >  2:256564/1‑73 (MQ=255)
                                                                                          gtgtCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTaaa                                                                                                      <  1:256564/73‑1 (MQ=255)
                                                                                          gtgtCTTTTCTGATACTCATTACACGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTAtt                                    >  2:1023348/1‑139 (MQ=255)
                                                                                             tCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCg                                 >  1:911952/1‑139 (MQ=255)
                                                                                                  tCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCggtggt                            <  1:1089498/139‑1 (MQ=255)
                                                                                                         cTCATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTc                     >  1:623802/1‑139 (MQ=255)
                                                                                                           cATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTc                                  <  1:216623/124‑1 (MQ=255)
                                                                                                           cATTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTc                                  >  2:216623/1‑124 (MQ=255)
                                                                                                            aTTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATggc                                           <  2:945953/114‑1 (MQ=255)
                                                                                                            aTTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATggc                                           >  1:945953/1‑114 (MQ=255)
                                                                                                            aTTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCggtgg                             <  2:1386800/128‑1 (MQ=255)
                                                                                                            aTTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCggtgg                             >  1:1386800/1‑128 (MQ=255)
                                                                                                            aTTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAAt                  >  1:643580/1‑139 (MQ=255)
                                                                                                            aTTACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAAt                  >  2:374571/1‑139 (MQ=255)
                                                                                                              tACAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAAttt                >  1:1340473/1‑139 (MQ=255)
                                                                                                                cAGGTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTgg              >  1:698526/1‑139 (MQ=255)
                                                                                                                  ggTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTggcg            <  2:854180/139‑1 (MQ=255)
                                                                                                                  ggTGTTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTggcg            <  2:623802/139‑1 (MQ=255)
                                                                                                                  ggTGTTAATCATTTTTCTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTggcg            <  1:1023348/139‑1 (MQ=255)
                                                                                                                   gtgtTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCa                                                   >  2:803087/1‑99 (MQ=255)
                                                                                                                   gtgtTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGtt                           <  2:568986/123‑1 (MQ=255)
                                                                                                                   gtgtTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGtt                           >  1:568986/1‑123 (MQ=255)
                                                                                                                   gtgtTAATCATTTTTGTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCa                                                   <  1:803087/99‑1 (MQ=255)
                                                                                                                    tgtTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTggcggc          >  2:572086/1‑139 (MQ=255)
                                                                                                                    tgtTAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTggcggc          <  2:1168214/139‑1 (MQ=255)
                                                                                                                      ttAATCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTGGCGGCAt        >  1:744209/1‑139 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTaaa                                                                                                      <  2:464876/43‑1 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTaaa                                                                                                      >  1:464876/1‑43 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGttt                                                                 <  2:717603/80‑1 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGttt                                                                 >  1:717603/1‑80 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATggc                                           <  1:1247422/102‑1 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATggc                                           >  2:1247422/1‑102 (MQ=255)
                                                                                                                        aaTCATTTTTTTGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTGGCGGCATCg      >  1:760078/1‑139 (MQ=255)
                                                                                                                             tttttttGGCTGCTTCTTTTAGCAAAGAAAGCATTAAatc                                                                                                    <  1:871822/40‑1 (MQ=255)
                                                                                                                             tttttttGGCTGCTTCTTTTAGCAAAGAAAGCATTAAatc                                                                                                    >  2:871822/1‑40 (MQ=255)
                                                                                                                              ttttttGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTGGCGGCATCGatat  >  1:777333/1‑137 (MQ=255)
                                                                                                                              ttttttGGCTGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTGGCGGCATCGatat  <  2:777333/137‑1 (MQ=255)
                                                                                                                                       |                                                                                                                               
TTTTTAAATGTGATAAACCTTATACCTTGAGTACATGGAGAGAATAATCGCTTATCAGACTTCAGGTACCTCAAAGAGTGTCTTTTTACCGTGTCTTTTCTGATACTCATTACAGGTGTTAATCATTTTTTTGGCCGCTTCTTTTAGCAAAGAAAGCATTAAATCATCATAATCAACGTAGAATCTGGTTGTTTCAGTTTCCGTTTTTATCTCACCGATGGCGGCTATTTCGGTGGTTAATTTCAATTTGGCGGCATCGATAT  >  NC_000913/1229429‑1229691

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A