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
A1 F1 I1 R1 773 79.9 4112934 92.2% 3792125 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,619,957 G→A *128* (TAG→TAA)  marA → multiple antibiotic resistance transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,619,9570GA100.0% 213.5 / NA 65*128* (TAG→TAA) marAmultiple antibiotic resistance transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (36/29);  total (36/29)

TCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATGT  >  NC_000913/1619835‑1620092
                                                                                                                          |                                                                                                                                       
tCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAAc                                                                                                                         <  2:1415094/139‑1 (MQ=255)
              gACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTg                                                                                                                  <  2:870411/132‑1 (MQ=255)
              gACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTg                                                                                                                  >  1:870411/1‑132 (MQ=255)
                   gAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGa                                                                                                                             <  2:1778248/116‑1 (MQ=255)
                   gAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGa                                                                                                                             >  1:1778248/1‑116 (MQ=255)
                                                             ggATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGt                                                                                                                       <  2:1828448/80‑1 (MQ=255)
                                                             ggATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGt                                                                                                                       >  1:1828448/1‑80 (MQ=255)
                                                              gATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTg                                                                           >  2:362725/1‑123 (MQ=255)
                                                              gATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTg                                                                           <  1:362725/123‑1 (MQ=255)
                                                                  aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTg                                                                                                                  >  1:1536657/1‑80 (MQ=255)
                                                                  aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTg                                                                                                                  <  2:1536657/80‑1 (MQ=255)
                                                                  aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATc                                                                                         >  2:677107/1‑105 (MQ=255)
                                                                  aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATc                                                                                         <  1:677107/105‑1 (MQ=255)
                                                                   ccAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGt                                                                                                                               >  2:382586/1‑66 (MQ=255)
                                                                   ccAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGt                                                                                                                               <  1:382586/66‑1 (MQ=255)
                                                                       tatGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAggg                                                  >  1:1070067/1‑139 (MQ=255)
                                                                           cAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGtt                                              <  1:1775520/139‑1 (MQ=255)
                                                                            aGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTg                                             >  1:267795/1‑139 (MQ=255)
                                                                             gggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGc                                            >  1:1647125/1‑139 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCtt                                                                      >  1:1001605/1‑112 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCtt                                                                      <  2:1001605/112‑1 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAggg                                                  >  1:1385897/1‑132 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAggg                                                  <  2:1385897/132‑1 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCg                                           >  1:292746/1‑139 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCg                                           >  1:1324169/1‑139 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCg                                           >  1:2012438/1‑139 (MQ=255)
                                                                              ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAACTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCg                                           >  1:511029/1‑139 (MQ=255)
                                                                                  aaTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGtt                                              >  1:375294/1‑132 (MQ=255)
                                                                                  aaTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGtt                                              <  2:375294/132‑1 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGaaa                                                                                                                                   >  2:1359327/1‑46 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGaaa                                                                                                                                   <  1:1359327/46‑1 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGa                                                                                                                             <  2:594538/52‑1 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGa                                                                                                                             >  1:594538/1‑52 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTg                                                                                                                  <  1:1187204/63‑1 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTg                                                                                                                  >  2:1187204/1‑63 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAggg                                                  <  2:361328/127‑1 (MQ=255)
                                                                                   aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAggg                                                  >  1:361328/1‑127 (MQ=255)
                                                                                             ttACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAg                            <  2:267795/139‑1 (MQ=255)
                                                                                                 aTCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAg                        <  2:2012438/139‑1 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTg                                                                           <  2:1617831/83‑1 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTg                                                                           >  1:1617831/1‑83 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATtct                                                                 >  1:34495/1‑93 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATtct                                                                 <  2:34495/93‑1 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGa                                         >  1:1709319/1‑117 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGa                                         <  2:1709319/117‑1 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACg                               >  1:766204/1‑127 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACg                               <  2:766204/127‑1 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAgttgtt                   >  2:214862/1‑139 (MQ=255)
                                                                                                      ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAgttgtt                   >  2:1338178/1‑139 (MQ=255)
                                                                                                              ttACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCa                                                                                           >  2:1927579/1‑59 (MQ=255)
                                                                                                              ttACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCa                                                                                           <  1:1927579/59‑1 (MQ=255)
                                                                                                              ttACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTtg           >  2:1708552/1‑139 (MQ=255)
                                                                                                               tACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCACAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCa                         <  2:1832660/124‑1 (MQ=255)
                                                                                                               tACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCACAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCa                         >  1:1832660/1‑124 (MQ=255)
                                                                                                                acaacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCAc                                >  1:628950/1‑116 (MQ=255)
                                                                                                                acaacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCAc                                <  2:628950/116‑1 (MQ=255)
                                                                                                                  aacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGcc       <  1:1708552/139‑1 (MQ=255)
                                                                                                                      gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGcc       >  2:1657757/1‑135 (MQ=255)
                                                                                                                      gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGcc       <  1:1657757/135‑1 (MQ=255)
                                                                                                                      gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATg   >  2:586335/1‑139 (MQ=255)
                                                                                                                       cTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTg                                             >  2:522883/1‑96 (MQ=255)
                                                                                                                       cTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTg                                             <  1:522883/96‑1 (MQ=255)
                                                                                                                       cTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGcc       >  1:833081/1‑134 (MQ=255)
                                                                                                                       cTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGcc       <  2:833081/134‑1 (MQ=255)
                                                                                                                       cTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATGt  >  1:474187/1‑139 (MQ=255)
                                                                                                                          |                                                                                                                                       
TCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATGT  >  NC_000913/1619835‑1620092

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A