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 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,736,276 C→T intergenic (+119/+77) xylR → / ← bax xylose divergent operon transcriptional activator/putative glucosaminidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,736,2760CT100.0% 175.4 / NA 55intergenic (+119/+77)xylR/baxxylose divergent operon transcriptional activator/putative glucosaminidase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/30);  total (25/30)

CGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGCGA  >  NC_000913/3736142‑3736399
                                                                                                                                       |                                                                                                                           
cGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCg                                                                                                                          >  2:418284/1‑139 (MQ=255)
   ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAg                                                                                                                       >  2:758799/1‑139 (MQ=255)
        tgttgtAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTGGTAGCTCaa                                                                                                                  <  1:1012548/139‑1 (MQ=39)
        tgttgtAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  <  1:1133641/139‑1 (MQ=39)
        tgttgtAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  <  1:418284/139‑1 (MQ=255)
                  aatgatgAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  >  1:802821/2‑129 (MQ=255)
                  aatgatgAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  <  2:802821/128‑1 (MQ=255)
                    tgatgaGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTgaga                                                                                                        <  2:170010/137‑1 (MQ=255)
                    tgatgaGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTgaga                                                                                                        >  1:170010/1‑137 (MQ=255)
                    tgatgaGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACa                                                                                                      >  1:376908/1‑139 (MQ=255)
                                tCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGcc                                                                                          >  1:494749/1‑139 (MQ=255)
                                   gCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTa                                                                                       <  2:769347/139‑1 (MQ=255)
                                     gTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATc                                                                                     <  2:376908/139‑1 (MQ=255)
                                      tCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATcc                                                                                    <  1:1410900/139‑1 (MQ=255)
                                       cacaTCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATc                                                                                     >  2:596206/1‑137 (MQ=255)
                                       cacaTCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATc                                                                                     <  1:596206/137‑1 (MQ=255)
                                                  aCGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACaa                                                                                                     <  2:341531/110‑1 (MQ=255)
                                                  aCGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACaa                                                                                                     >  1:341531/1‑110 (MQ=255)
                                                    gCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  <  2:1328990/95‑1 (MQ=255)
                                                    gCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  >  1:1328990/1‑95 (MQ=255)
                                                      tGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGAt                                                                    <  2:494749/139‑1 (MQ=255)
                                                                tCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTCACAAGTCGGATAAGGCTCAAg                                                          >  2:375792/1‑139 (MQ=255)
                                                                       cggcgTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGc                                                   >  1:1368888/1‑139 (MQ=255)
                                                                          cgTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAAt                                                >  2:1075950/1‑139 (MQ=255)
                                                                                           aCCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACa                                                                                                      <  1:1161888/68‑1 (MQ=255)
                                                                                           aCCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACa                                                                                                      >  2:1161888/1‑68 (MQ=255)
                                                                                               aCCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAAt                                                     >  2:372326/1‑113 (MQ=255)
                                                                                               aCCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAAt                                                     <  1:372326/113‑1 (MQ=255)
                                                                                                cccGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGaaa                                                      <  1:1485937/111‑1 (MQ=255)
                                                                                                cccGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGaaa                                                      >  2:1485937/1‑111 (MQ=255)
                                                                                                cccGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAAcc                          <  1:758799/139‑1 (MQ=255)
                                                                                                 ccGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCg                         >  2:1291294/1‑139 (MQ=255)
                                                                                                      aGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGt                    <  2:1076310/139‑1 (MQ=255)
                                                                                                      aGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGt                    <  2:1368888/139‑1 (MQ=255)
                                                                                                      aGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGt                    <  1:1075950/139‑1 (MQ=255)
                                                                                                      aGGCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTCACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGt                    <  1:375792/139‑1 (MQ=255)
                                                                                                       ggCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTgaga                                                                                                        >  1:1048756/1‑54 (MQ=255)
                                                                                                       ggCATGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTgaga                                                                                                        <  2:1048756/54‑1 (MQ=255)
                                                                                                          aTGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  >  2:61868/1‑41 (MQ=255)
                                                                                                          aTGATAAAACGCACCAACAACGCTTCAGGTTCGTAGCTCaa                                                                                                                  <  1:61868/41‑1 (MQ=255)
                                                                                                                   cGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATgcg                                      >  1:1450788/1‑108 (MQ=255)
                                                                                                                   cGCACCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATgcg                                      <  2:1450788/108‑1 (MQ=255)
                                                                                                                      aCCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCt                                                              >  2:89870/1‑81 (MQ=255)
                                                                                                                      aCCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCt                                                              <  1:89870/81‑1 (MQ=255)
                                                                                                                      aCCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATgcgc                                     >  1:592200/1‑106 (MQ=255)
                                                                                                                      aCCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATgcgc                                     <  2:592200/106‑1 (MQ=255)
                                                                                                                      aCCAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGc    >  2:370757/1‑139 (MQ=255)
                                                                                                                       ccAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTgg                     <  1:376381/121‑1 (MQ=255)
                                                                                                                       ccAACAACGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTgg                     >  2:376381/1‑121 (MQ=255)
                                                                                                                        caacaaCGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTTGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAAcc                          <  2:1180355/115‑1 (MQ=255)
                                                                                                                        caacaaCGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTTGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAAcc                          >  1:1180355/1‑115 (MQ=255)
                                                                                                                        caacaaCGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGCGa  <  1:370757/139‑1 (MQ=255)
                                                                                                                              cGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTa                  <  1:270413/117‑1 (MQ=255)
                                                                                                                              cGCTTCAGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTa                  >  2:270413/1‑117 (MQ=255)
                                                                                                                                    aGGTTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAAt                                                     <  2:379731/76‑1 (MQ=255)
                                                                                                                                       |                                                                                                                           
CGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGGCTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGCGA  >  NC_000913/3736142‑3736399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A