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 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,759,132 A→G I50V (ATT→GTT)  yfjI → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,759,1320AG95.5% 215.7 / 0.6 66I50V (ATT→GTT) yfjICP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base A (2/1);  new base G (28/35);  total (30/36)
Fisher's exact test for biased strand distribution p-value = 5.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.23e-01

GAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAA  >  NC_000913/2759035‑2759227
                                                                                                 |                                                                                               
gAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGtt                                                                                               <  2:323670/100‑1 (MQ=255)
  aTGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGa                                                                                             >  1:136090/1‑100 (MQ=255)
    gCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATg                                                                                           >  1:689071/1‑100 (MQ=255)
    gCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATg                                                                                           <  1:630113/100‑1 (MQ=255)
        tttATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTg                                                                                       <  1:790837/100‑1 (MQ=255)
             gAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGAt                                                                                  >  1:849802/1‑100 (MQ=255)
             gAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGAt                                                                                  >  1:489550/1‑100 (MQ=255)
              aaGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGAtt                                                                                 <  1:997328/100‑1 (MQ=255)
              aaGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGAtt                                                                                 >  1:480965/1‑100 (MQ=255)
               aGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTg                                                                                <  2:409827/100‑1 (MQ=255)
               aGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTg                                                                                <  1:77198/100‑1 (MQ=255)
                  ggAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGaat                                                                             >  2:122217/1‑100 (MQ=255)
                  ggAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGaat                                                                             <  1:44088/100‑1 (MQ=255)
                   gAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGaata                                                                            >  1:1007134/1‑100 (MQ=255)
                     aCAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGaataat                                                                          >  2:462572/1‑100 (MQ=255)
                      cAGTATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGTGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATc                                                                         <  2:263854/100‑1 (MQ=255)
                       aGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCt                                                                        <  1:408034/100‑1 (MQ=255)
                       aGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCt                                                                        >  2:630354/1‑100 (MQ=255)
                        gCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTa                                                                       <  2:339536/100‑1 (MQ=255)
                           tACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGt                                                                    >  1:988855/1‑100 (MQ=255)
                                 ggCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGTGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGccc                                                               <  2:228435/99‑1 (MQ=255)
                                  gCCCCTCAAGGTTTGATTGCTGGTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGTTGTTTGCCGATTGAATAATCTACGTGGGCCgg                                                             >  2:235948/1‑100 (MQ=255)
                                    cccTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTa                                                           <  2:360722/100‑1 (MQ=255)
                                        cAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCAc                                                       <  2:480961/100‑1 (MQ=255)
                                            gTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACtttt                                                   <  2:56793/100‑1 (MQ=255)
                                               tGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCtt                                                <  2:1181843/100‑1 (MQ=255)
                                                gATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTa                                               >  2:1124209/1‑100 (MQ=255)
                                                  ttGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAAt                                             <  1:1278872/100‑1 (MQ=255)
                                                   tgctgcTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATg                                            <  1:630358/100‑1 (MQ=255)
                                                         ttCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTg                                      <  1:122219/100‑1 (MQ=255)
                                                         ntCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTg                                      >  2:326650/2‑100 (MQ=255)
                                                          tCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTgg                                     <  2:826886/100‑1 (MQ=255)
                                                           cTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGc                                    >  2:410738/1‑100 (MQ=255)
                                                           cTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGc                                    <  1:1143985/100‑1 (MQ=255)
                                                           cTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGc                                    >  2:722963/1‑100 (MQ=255)
                                                              ctctTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGa                                 >  1:826359/1‑100 (MQ=255)
                                                               tctTGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGaa                                >  2:819888/1‑100 (MQ=255)
                                                                 ttGGGGTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATc                              <  2:617041/100‑1 (MQ=255)
                                                                   ggggTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAg                            <  2:484748/100‑1 (MQ=255)
                                                                   ggggTAATTTCTCTTGCCTGTCAGAACCGAGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGCTATCACTTTTCTTAATGACTCTGGCTGAATCAg                            <  2:786508/100‑1 (MQ=255)
                                                                    gggTAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAgg                           <  1:530353/100‑1 (MQ=255)
                                                                       tAATTTCTCTTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGa                        <  2:973596/100‑1 (MQ=255)
                                                                             ctctTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCGCTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTaa                  >  2:710370/1‑100 (MQ=255)
                                                                             ctctTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTaa                  >  1:207769/1‑100 (MQ=255)
                                                                             ctctTGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTaa                  >  1:914032/1‑100 (MQ=255)
                                                                                 tGCCTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGt              >  2:310296/1‑100 (MQ=255)
                                                                                    cTGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACg           >  2:343886/1‑100 (MQ=255)
                                                                                    cTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACg           >  1:828292/1‑100 (MQ=255)
                                                                                     tGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACgg          >  1:88521/1‑100 (MQ=255)
                                                                                     tGTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACgg          <  2:992986/100‑1 (MQ=255)
                                                                                      gTCCGAACCGGGTTGATGTTTGCCGATTGAATAATGTACGTTGACCGGTATCAGTTTTCTTAATGACTATGGCTGAATCAGGCGAACGTAAGAGTACg           >  1:316477/1‑98 (MQ=255)
                                                                                      gTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGt         <  2:208377/100‑1 (MQ=255)
                                                                                      gTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGt         <  2:594749/100‑1 (MQ=255)
                                                                                      gTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGt         <  2:572618/100‑1 (MQ=255)
                                                                                      gTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGt         >  2:485365/1‑100 (MQ=255)
                                                                                      gTCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGt         >  1:774122/1‑100 (MQ=255)
                                                                                       tCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGGCTCTGGCTGAATCAGGTGAACGTAAGAGTACGGtt        <  2:1115578/100‑1 (MQ=255)
                                                                                       tCAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGtt        <  2:190740/100‑1 (MQ=255)
                                                                                        cAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGtt        <  2:1115552/99‑1 (MQ=255)
                                                                                        cAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTg       <  1:1067026/100‑1 (MQ=255)
                                                                                        cAGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTg       >  1:524100/1‑100 (MQ=255)
                                                                                         aGAACCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGACTGAATTAGGTGAACGTTGGTGTATGGTTg       >  2:1170539/1‑99 (MQ=255)
                                                                                         aGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGa      <  1:512442/100‑1 (MQ=255)
                                                                                           aaCCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATa    <  2:136088/100‑1 (MQ=255)
                                                                                            aCCGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATaa   <  1:484851/100‑1 (MQ=255)
                                                                                             ccGGGTTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATAACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTAGATaaa  >  1:403505/1‑100 (MQ=255)
                                                                                                 |                                                                                               
GAATGCAATTTATGAAGTGGAACAGCATACGCAGGCCCCTCAAGGTTTGATTGCTGCTTCTGCTCTTGGGGTAATTTCTCTTGCCTGTCAGAACCGGATTGATGTTTGCCGATTGAATAATCTACGTGGCCCGGTATCACTTTTCTTAATGACTCTGGCTGAATCAGGTGAACGTAAGAGTACGGTTGATAAA  >  NC_000913/2759035‑2759227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A