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
A6 F1 I1 R1 750 51.0 2595496 93.6% 2429384 106.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,515,726 T→C Y63C (TAT→TGT)  dam ← DNA adenine methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,515,7260TC100.0% 205.9 / NA 57Y63C (TAT→TGT) damDNA adenine methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/28);  total (29/28)

CCCGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTATAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAATA  >  NC_000913/3515592‑3515854
                                                                                                                                      |                                                                                                                                
cccGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACagag                                                                                                                              >  1:971709/1‑139 (MQ=255)
cccGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACagag                                                                                                                              >  1:909080/1‑139 (MQ=255)
cccGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACagag                                                                                                                              >  1:536948/1‑139 (MQ=255)
 ccGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAgaga                                                                                                                             <  2:214131/139‑1 (MQ=255)
          cggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAgg                                                                                                                    <  1:666485/139‑1 (MQ=255)
           ggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  2:909080/139‑1 (MQ=255)
           ggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  2:73485/139‑1 (MQ=255)
                      tttGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGata                                                                                                        <  2:536948/139‑1 (MQ=255)
                           tgAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGc                                                                                                   <  2:971709/139‑1 (MQ=255)
                            gAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  <  2:533554/139‑1 (MQ=255)
                             aaCTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGc                                                                                                   >  1:1227749/1‑137 (MQ=255)
                             aaCTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGc                                                                                                   <  2:1227749/137‑1 (MQ=255)
                                   tCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGatat                                                                                           >  2:1098108/1‑139 (MQ=255)
                                       ggAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACg                                                                                       >  1:699608/1‑139 (MQ=255)
                                               tAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               <  1:1098108/139‑1 (MQ=255)
                                                     aCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGAt                                                                                                                        <  2:616192/92‑1 (MQ=255)
                                                     aCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGAt                                                                                                                        >  1:616192/1‑92 (MQ=255)
                                                     aCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGgtgt                                                                         >  2:471810/1‑139 (MQ=255)
                                                        tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGata                                                                                                        >  2:239711/1‑105 (MQ=255)
                                                        tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGata                                                                                                        <  1:239711/105‑1 (MQ=255)
                                                        tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTga                                                                      >  1:272631/1‑139 (MQ=255)
                                                        tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTga                                                                      >  1:1119200/1‑139 (MQ=255)
                                                          ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGtt                                                                        >  2:892008/1‑135 (MQ=255)
                                                          ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGtt                                                                        <  1:892008/135‑1 (MQ=255)
                                                                       tCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCgg                                                       <  2:699608/139‑1 (MQ=255)
                                                                                    gCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAgg                                          <  2:1119200/139‑1 (MQ=255)
                                                                                     cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCt                                                                                                               <  2:97238/69‑1 (MQ=255)
                                                                                     cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCt                                                                                                               >  1:97238/1‑69 (MQ=255)
                                                                                     cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGc                                         >  2:835797/1‑139 (MQ=255)
                                                                                     cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGc                                         >  1:777717/1‑139 (MQ=255)
                                                                                         cgTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGa                                                                                                          >  1:157627/1‑70 (MQ=255)
                                                                                         cgTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGa                                                                                                          <  2:157627/70‑1 (MQ=255)
                                                                                           tGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAAcc                                   >  1:552084/1‑139 (MQ=255)
                                                                                                    tacgtacTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCg                          >  2:1204272/1‑139 (MQ=255)
                                                                                                          cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCg                                                                                                                 <  1:517616/46‑1 (MQ=255)
                                                                                                          cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCg                                                                                                                 >  2:517616/1‑46 (MQ=255)
                                                                                                          cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCg                                                        >  2:584644/1‑103 (MQ=255)
                                                                                                          cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCg                                                        <  1:584644/103‑1 (MQ=255)
                                                                                                          cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTg                    >  1:800301/1‑139 (MQ=255)
                                                                                                          cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTg                    >  2:217336/1‑139 (MQ=255)
                                                                                                             atcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGc                 >  2:291187/1‑139 (MQ=255)
                                                                                                              tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAgg                                          >  2:8507/1‑113 (MQ=255)
                                                                                                              tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAgg                                          <  1:8507/113‑1 (MQ=255)
                                                                                                              tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCa                >  2:279750/1‑139 (MQ=255)
                                                                                                              tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTAGGCa                >  2:398062/1‑139 (MQ=255)
                                                                                                                aGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCaaa              <  2:800301/139‑1 (MQ=255)
                                                                                                                  tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            <  2:552084/139‑1 (MQ=255)
                                                                                                                  tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            <  1:471810/139‑1 (MQ=255)
                                                                                                                  tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            <  1:279750/139‑1 (MQ=255)
                                                                                                                          ttCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTaa    <  1:1291439/139‑1 (MQ=255)
                                                                                                                            ctcaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGTTATAACGGGAAAAGTCGGTGTTGAGAAACACCTACCCGGCTCCAACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAata  <  2:313491/137‑1 (MQ=255)
                                                                                                                            cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACaa                                              <  2:45687/95‑1 (MQ=255)
                                                                                                                            cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACaa                                              >  1:45687/1‑95 (MQ=255)
                                                                                                                            cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAata  <  1:1204272/139‑1 (MQ=255)
                                                                                                                            cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGGTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAata  >  2:756138/1‑139 (MQ=255)
                                                                                                                                   ttACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAATGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAAt             <  1:778314/121‑1 (MQ=255)
                                                                                                                                   ttACAGAGACTGATCAGGTCGATATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAGGGCTCAACCAGACATTCGCCCTTGGGCAAAt             >  2:778314/1‑121 (MQ=255)
                                                                                                                                      |                                                                                                                                
CCCGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTATAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAATA  >  NC_000913/3515592‑3515854

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A