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
A11 F1 I2 R1 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,770,404 G→A *234* (TAG→TAA)  yfjR → CP4‑57 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,770,4040GA100.0% 205.1 / NA 65*234* (TAG→TAA) yfjRCP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/37);  total (28/37)

TGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCC  >  NC_000913/2770268‑2770525
                                                                                                                                        |                                                                                                                         
tGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTTCGGCCGACAGCCCACCGGAATAacg                                                                                                                         >  1:54144/1‑139 (MQ=255)
tGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacg                                                                                                                         >  1:1380800/1‑139 (MQ=255)
tGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacg                                                                                                                         <  1:1320797/139‑1 (MQ=255)
     gagaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGc                                                                                                                    >  1:1294679/1‑139 (MQ=255)
              cgccgcAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATc                                                                                                           <  1:564948/139‑1 (MQ=255)
                  gcAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacg                                                                                                                         <  1:1578409/121‑1 (MQ=255)
                    aaTGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                     <  2:1380800/139‑1 (MQ=255)
                     aTGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    <  1:1225310/139‑1 (MQ=255)
                          aGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACa                                                                                               <  2:1156374/139‑1 (MQ=255)
                              tgtgTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATgga                                                                                           <  1:244356/139‑1 (MQ=255)
                                    gCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    >  2:1097355/1‑124 (MQ=255)
                                    gCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    <  1:1097355/124‑1 (MQ=255)
                                    gCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                     >  1:894173/1‑139 (MQ=255)
                                    gCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCACTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCAGGCCGACAGCCCACCGGAATCACGCAGGCGTTGTTATCAACCCGGCAACATGGATGAGcc                                                                                     >  2:687305/1‑139 (MQ=255)
                                     ccTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGccc                                                                                    <  2:894173/139‑1 (MQ=255)
                                        ggTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGt                                                                                 >  1:1067433/1‑139 (MQ=255)
                                        ggTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGt                                                                                 <  2:74216/139‑1 (MQ=255)
                                           tGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                              <  2:131515/139‑1 (MQ=255)
                                                   cGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTg                                                                      <  1:1460549/139‑1 (MQ=255)
                                                    ggTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGc                                                                     >  2:1187051/1‑139 (MQ=255)
                                                                ggCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCAt                                                         >  2:1493755/1‑139 (MQ=255)
                                                                     tACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                               <  2:366791/112‑1 (MQ=255)
                                                                     tACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                               >  1:366791/1‑112 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTa                                                                                                             <  2:267679/81‑1 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTa                                                                                                             >  1:267679/1‑81 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    >  1:1405622/1‑90 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    <  2:1405622/90‑1 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggagg                                                                                         >  1:1654839/1‑101 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggagg                                                                                         <  2:1654839/101‑1 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTat                                                   >  2:902804/1‑139 (MQ=255)
                                                                         ccATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                <  1:1065376/139‑1 (MQ=255)
                                                                         ccATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                <  1:902804/139‑1 (MQ=255)
                                                                              ttCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGtca                                           <  1:1493755/139‑1 (MQ=255)
                                                                                      aTCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                               <  1:690888/111‑1 (MQ=255)
                                                                                      aTCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                               >  2:690888/1‑111 (MQ=255)
                                                                                      aTCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                <  2:950264/126‑1 (MQ=255)
                                                                                      aTCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                >  1:950264/1‑126 (MQ=255)
                                                                                      aTCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTg                                   >  1:1582029/1‑139 (MQ=255)
                                                                                        ccAGCATTCACTGCTTACGTTTGTTTCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                 <  2:54144/139‑1 (MQ=255)
                                                                                        ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                 <  1:1187051/139‑1 (MQ=255)
                                                                                            cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                     >  2:1007082/1‑83 (MQ=255)
                                                                                            cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCTATTATCGCCATTGTTat                                                   >  2:284676/1‑117 (MQ=255)
                                                                                            cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCTATTATCGCCATTGTTat                                                   <  1:284676/117‑1 (MQ=255)
                                                                                            cATTCACTGCATACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                     <  1:1007082/83‑1 (MQ=255)
                                                                                                cACTGCTTACGTTTGTTCAGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTAACAACCCGGCAACATGGAGGGGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCg                         <  1:687305/139‑1 (MQ=255)
                                                                                                 aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACa                                                                                               <  1:1428999/68‑1 (MQ=255)
                                                                                                 aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACa                                                                                               >  2:1428999/1‑68 (MQ=255)
                                                                                                   tGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCg                         <  1:339059/136‑1 (MQ=255)
                                                                                                   tGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCg                         >  2:339059/1‑136 (MQ=255)
                                                                                                     cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    <  1:1002231/59‑1 (MQ=255)
                                                                                                     cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                    >  2:1002231/1‑59 (MQ=255)
                                                                                                     cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGtt                                                     >  2:1322697/1‑106 (MQ=255)
                                                                                                     cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGtt                                                     <  1:1322697/106‑1 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgt                                                                                                                  <  1:1326578/44‑1 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgt                                                                                                                  >  2:1326578/1‑44 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTat                                                   <  1:995987/107‑1 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTat                                                   >  2:995987/1‑107 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAg                      >  2:227210/1‑136 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAg                      <  1:227210/136‑1 (MQ=255)
                                                                                                        aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGt                                                                                 >  1:826907/1‑75 (MQ=255)
                                                                                                        aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGt                                                                                 <  2:826907/75‑1 (MQ=255)
                                                                                                        aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                              >  2:1637331/1‑78 (MQ=255)
                                                                                                        aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                              <  1:1637331/78‑1 (MQ=255)
                                                                                                                  cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa       <  2:1582029/139‑1 (MQ=255)
                                                                                                                    gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACg     >  1:747815/1‑139 (MQ=255)
                                                                                                                    gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACg     <  1:852069/139‑1 (MQ=255)
                                                                                                                       gACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGcc  <  2:1010078/139‑1 (MQ=255)
                                                                                                                               aCCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                               <  1:513181/70‑1 (MQ=255)
                                                                                                                               aCCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                               >  2:513181/1‑70 (MQ=255)
                                                                                                                                        |                                                                                                                         
TGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCC  >  NC_000913/2770268‑2770525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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