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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,101,039 (C)7→8 coding (585/720 nt) yggN ← DUF2884 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,101,0321.C100.0% 167.3 / NA 49L198V (CTG→GTG) yggNDUF2884 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (23/26);  total (23/26)

AATAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGGCG  >  NC_000913/3100895‑3101165
                                                                                                                                          |                                                                                                                                      
aaTAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                      <  1:833332/139‑1 (MQ=255)
          tattTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑ccccccccagg                                                                                                                            <  2:1122535/139‑5 (MQ=255)
                   ttCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGc                                                                                                                    <  1:1273118/139‑1 (MQ=255)
                             gggCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTa                                                                                                          >  1:909517/1‑139 (MQ=255)
                             gggCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                      >  1:1426528/1‑110 (MQ=255)
                             gggCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                      <  2:1426528/110‑1 (MQ=255)
                                   tGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCCCAGGCTTCCCAGCACATTCTGTAATggg                                                                                                     >  1:329081/1‑139 (MQ=255)
                                   tGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGt                                                                                                    >  1:1215865/1‑139 (MQ=255)
                                   tGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑cccccc                                                                                                                                 <  1:1248792/109‑1 (MQ=255)
                                   tGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑cccccc                                                                                                                                 >  2:1248792/1‑109 (MQ=255)
                                    gCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGtt                                                                                                   >  2:127214/1‑139 (MQ=255)
                                          aTCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgcc                                                                                             >  2:1433540/1‑139 (MQ=255)
                                           tCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            <  2:1215865/139‑1 (MQ=255)
                                                     tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCa                                                                                  >  1:1553788/1‑139 (MQ=255)
                                                     tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                      <  1:1494973/86‑1 (MQ=255)
                                                     tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                      >  2:1494973/1‑86 (MQ=255)
                                                       acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCAcc                                                                                >  1:955850/1‑139 (MQ=255)
                                                       acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGACGCTTTTCAGCAcc                                                                                >  2:1284294/1‑139 (MQ=255)
                                                         aaCGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACAt                                                                                                                <  1:1491541/105‑1 (MQ=255)
                                                         aaCGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACAt                                                                                                                >  2:1491541/1‑105 (MQ=255)
                                                               gCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTcgc                                                                        >  2:142953/1‑139 (MQ=255)
                                                                cTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTcgcg                                                                       <  1:1433540/139‑1 (MQ=255)
                                                                 tACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTcgcg                                                                       <  2:329081/139‑1 (MQ=255)
                                                                      aCATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGATTTTCAGCACCGCTTTCGCGCCCAt                                                                  <  2:404346/139‑1 (MQ=255)
                                                                          cTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGc                                                                                                                    <  2:1215903/84‑1 (MQ=255)
                                                                          cTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGc                                                                                                                    >  1:1215903/1‑84 (MQ=255)
                                                                          cTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAt                                                             <  2:955850/139‑1 (MQ=255)
                                                                             tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCGCATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCg                                                                               >  1:1298253/1‑118 (MQ=255)
                                                                             tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCGCATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCg                                                                               <  2:1298253/118‑1 (MQ=255)
                                                                             tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTc                                                                                                              >  1:802933/1‑87 (MQ=255)
                                                                             tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTc                                                                                                              <  2:802933/87‑1 (MQ=255)
                                                                             tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTaa                                                          >  1:1009292/1‑139 (MQ=255)
                                                                               ccAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  2:1204428/139‑1 (MQ=255)
                                                                                    ctgctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTACTGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTc                                                   >  2:307277/1‑139 (MQ=255)
                                                                                       ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTg                                                <  1:127214/139‑1 (MQ=255)
                                                                                               cTTTTTTCTGCTTTTTCCTCTCGGTTTGGATTGAGTATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTc                                        <  1:307277/139‑1 (MQ=255)
                                                                                                  tttCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCAc                                     <  2:909517/139‑1 (MQ=255)
                                                                                                   ttCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCAcc                                    <  2:1604402/139‑1 (MQ=255)
                                                                                                        gCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTg                               >  1:229615/1‑139 (MQ=255)
                                                                                                            tttCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGca                                                                                                                   >  1:596142/1‑51 (MQ=255)
                                                                                                            tttCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGca                                                                                                                   <  2:596142/51‑1 (MQ=255)
                                                                                                             ttCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGa                          <  1:780965/139‑1 (MQ=255)
                                                                                                             ttCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGACGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGa                          <  1:1284294/139‑1 (MQ=255)
                                                                                                               ccACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGAtt                        <  2:1553788/139‑1 (MQ=255)
                                                                                                                    cGGTTTGGATTGAGGATTGCAGCCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACt                    <  2:752201/139‑1 (MQ=255)
                                                                                                                          ggATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  2:1194531/96‑1 (MQ=255)
                                                                                                                          ggATTGAGGATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        >  1:1194531/1‑96 (MQ=255)
                                                                                                                                aGGATTGCAGC‑CCCCCCCAGGCTTCCTAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCtt       >  2:311828/1‑139 (MQ=255)
                                                                                                                                 ggATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            >  1:916990/1‑53 (MQ=255)
                                                                                                                                 ggATTGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            <  2:916990/53‑1 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgc                                                                                              >  2:1102804/1‑47 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgc                                                                                              <  1:1102804/47‑1 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  <  2:1086594/75‑1 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  >  2:461801/1‑75 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  <  1:461801/75‑1 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  >  1:1086594/1‑75 (MQ=255)
                                                                                                                                     tGCAGC‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGgcg  <  1:142953/139‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                      
AATAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGGCG  >  NC_000913/3100895‑3101165

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A