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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

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% 215.2 / NA 67*234* (TAG→TAA) yfjRCP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/36);  total (31/36)

TGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGAC  >  NC_000913/2770268‑2770530
                                                                                                                                        |                                                                                                                              
tGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacg                                                                                                                              >  1:1290154/1‑139 (MQ=255)
   aGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           <  1:193993/139‑1 (MQ=255)
   aGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           <  2:140810/139‑1 (MQ=255)
   aGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           <  1:1411793/139‑1 (MQ=255)
      agaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                        >  1:504813/1‑139 (MQ=255)
      agaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                        <  2:1479906/139‑1 (MQ=255)
          ttttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAgg                                                                                                                          >  2:142122/1‑133 (MQ=255)
          ttttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAgg                                                                                                                          <  1:142122/133‑1 (MQ=255)
          ttttCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgttgt                                                                                                                    >  1:814863/1‑139 (MQ=255)
                  gcAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAAcc                                                                                                            <  2:1290154/139‑1 (MQ=255)
                  gcAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAAcc                                                                                                            <  2:17552/139‑1 (MQ=255)
                    aaTGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                          >  2:437600/1‑139 (MQ=255)
                    aaTGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACCTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                          <  2:1088280/139‑1 (MQ=255)
                              tgtgTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATgga                                                                                                >  1:1454408/1‑139 (MQ=255)
                                tgtCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggagg                                                                                              >  2:1583619/1‑139 (MQ=255)
                                tgtCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggagg                                                                                              >  2:1452001/1‑139 (MQ=255)
                                 gtCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgt                                                                                                                       <  2:1138281/113‑1 (MQ=255)
                                 gtCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATCTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgt                                                                                                                       >  1:1138281/1‑113 (MQ=255)
                                        ggTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGt                                                                                      >  1:280988/1‑139 (MQ=255)
                                          ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                                    >  1:1547606/1‑139 (MQ=255)
                                                       cTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCAt                                                                       <  1:1583619/139‑1 (MQ=255)
                                                          cattcaGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                    <  2:1536007/139‑1 (MQ=255)
                                                          cattcaGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                    <  2:814863/139‑1 (MQ=255)
                                                               aGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCa                                                               >  2:1429759/1‑139 (MQ=255)
                                                                ggCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           <  1:1455505/78‑1 (MQ=255)
                                                                ggCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           >  2:1455505/1‑78 (MQ=255)
                                                                    ttcccccATTTGCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGGCAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGtt                                                          >  1:933789/4‑139 (MQ=255)
                                                                     tACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTa                                                         <  2:280988/139‑1 (MQ=255)
                                                                     tACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTa                                                         <  2:561919/139‑1 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                >  1:1071993/1‑131 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                <  2:1071993/131‑1 (MQ=255)
                                                                      aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTat                                                        >  1:1293819/1‑139 (MQ=255)
                                                                           aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                         <  1:1198049/85‑1 (MQ=255)
                                                                           aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                         >  2:1198049/1‑85 (MQ=255)
                                                                           aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                  >  1:41481/1‑124 (MQ=255)
                                                                           aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                  <  2:41481/124‑1 (MQ=255)
                                                                           aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTa                                                         <  1:544354/133‑1 (MQ=255)
                                                                           aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTa                                                         >  2:544354/1‑133 (MQ=255)
                                                                              ttCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTAGTGCCATTATCGCCATTGTTATCATCGtca                                                <  1:931376/139‑1 (MQ=255)
                                                                                 gCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCTACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                >  2:978765/1‑120 (MQ=255)
                                                                                 gCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                <  1:978765/120‑1 (MQ=255)
                                                                                        ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                      <  2:1293819/139‑1 (MQ=255)
                                                                                        ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                      <  1:1429759/139‑1 (MQ=255)
                                                                                        ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                      <  1:1452001/139‑1 (MQ=255)
                                                                                        ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                      <  1:77691/139‑1 (MQ=255)
                                                                                               tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           <  2:788096/47‑1 (MQ=255)
                                                                                               tCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                           >  1:788096/1‑47 (MQ=255)
                                                                                                 aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                         >  1:1130018/1‑63 (MQ=255)
                                                                                                 aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                         <  2:1130018/63‑1 (MQ=255)
                                                                                                 aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                          >  2:1449450/1‑62 (MQ=255)
                                                                                                 aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                          <  1:1449450/62‑1 (MQ=255)
                                                                                                    gCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                                   <  1:249132/82‑1 (MQ=255)
                                                                                                    gCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGcc                                                                                   >  2:249132/1‑82 (MQ=255)
                                                                                                     cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                     >  2:1141995/1‑111 (MQ=255)
                                                                                                     cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                     <  1:1141995/111‑1 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCaa                                                                                                              <  1:860275/53‑1 (MQ=255)
                                                                                                      ttACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCaa                                                                                                              >  2:860275/1‑53 (MQ=255)
                                                                                                        aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgtt                                                                                                                      >  1:322129/1‑43 (MQ=255)
                                                                                                        aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgtt                                                                                                                      <  2:322129/43‑1 (MQ=255)
                                                                                                             tGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAg                 >  2:827484/1‑139 (MQ=255)
                                                                                                               ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                    >  2:607916/1‑86 (MQ=255)
                                                                                                               ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                    <  1:607916/86‑1 (MQ=255)
                                                                                                               ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGcc               >  1:850993/1‑139 (MQ=255)
                                                                                                                  cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa            <  1:437600/139‑1 (MQ=255)
                                                                                                                    gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                          >  1:1543994/1‑59 (MQ=255)
                                                                                                                    gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                          <  2:1543994/59‑1 (MQ=255)
                                                                                                                    gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACg          >  2:1328846/1‑139 (MQ=255)
                                                                                                                            cccACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGac  <  2:35632/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                              
TGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGAC  >  NC_000913/2770268‑2770530

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