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
A1 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,736,160 +A intergenic (+3/+193) 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_0009133,736,1591.A100.0% 180.3 / NA 55intergenic (+2/+194)xylR/baxxylose divergent operon transcriptional activator/putative glucosaminidase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (33/22);  total (33/22)

TCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAG  >  NC_000913/3736032‑3736282
                                                                                                                                |                                                                                                                           
tCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGaa                                                                                                                   <  1:138115/139‑1 (MQ=255)
  gATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAAtt                                                                                                                 >  1:670463/1‑139 (MQ=255)
    tCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATTTTTCTACTCTGTTTTTAAAACAGCATATGCCACGACGCCAAAAGAGTATAGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAAgtgt                                                                                                               >  2:191252/1‑139 (MQ=255)
      aaTGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCg                                                                                                             >  1:155321/1‑139 (MQ=255)
      aaTGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCg                                                                                                             <  2:670463/139‑1 (MQ=255)
          agaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑a                                                                                                                            <  2:332765/119‑1 (MQ=255)
          agaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑a                                                                                                                            >  1:332765/1‑119 (MQ=255)
              atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCg                                                                                                          <  2:449238/134‑1 (MQ=255)
              atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCg                                                                                                          >  1:449238/1‑134 (MQ=255)
                cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATc                                                                                                   >  2:862456/1‑139 (MQ=255)
                                       cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      <  1:1108524/129‑1 (MQ=255)
                                       cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      >  2:1108524/1‑129 (MQ=255)
                                       cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCgg                                                                            >  2:309976/1‑139 (MQ=255)
                                          cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      <  1:207545/126‑1 (MQ=255)
                                          cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      >  2:207545/1‑126 (MQ=255)
                                           aaTATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgc                                                                        <  1:309976/139‑1 (MQ=255)
                                                 tCTACTCTGTTTTAAAAAAAGCATATGCCACGACGCC‑AAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGa                                                                 <  1:539081/139‑1 (MQ=255)
                                                        tGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGt                                                                               >  1:1086242/1‑119 (MQ=255)
                                                        tGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGt                                                                               <  2:1086242/119‑1 (MQ=255)
                                                         gTTTTTAAAAAAGCATATGACACGACGCC‑AAAGAGTATCGCGATGGAAATAGCGAGGTCATGGTGTAACGAATGATGAGAATTGTCGGCGTCCCATCAGGTAACGCTGCGTGGTTGTTGGATGGGGCGGGAACGCCTTa                                                         >  2:539081/1‑139 (MQ=255)
                                                                    aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTAc                                               >  2:327904/1‑139 (MQ=255)
                                                                      agacagACACGACGCCAAAAGAGTATAGCGATGTAAATAGCGAGGTCATGTTGTAACGAATCATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTAccc                                             <  2:721570/134‑1 (MQ=38)
                                                                                 acgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCTGCCAGGCATGa                                  >  2:760280/1‑139 (MQ=255)
                                                                                  cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                >  2:525875/1‑124 (MQ=255)
                                                                                  cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                <  1:525875/124‑1 (MQ=255)
                                                                                  cgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACAGCAGGTAACACTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGAt                                 >  2:379496/1‑139 (MQ=39)
                                                                                       aaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                     >  2:17390/1‑66 (MQ=255)
                                                                                       aaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                     <  1:17390/66‑1 (MQ=255)
                                                                                       aaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGAAACGAATGATGAGAATTGTCGGCGTCGCATCAGGTAACGCTGCGTGGTTGGCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGactgtct                            >  1:721570/1‑133 (MQ=38)
                                                                                               tCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaac                    >  2:442639/1‑139 (MQ=255)
                                                                                                  cgATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTa                                                         <  2:685764/99‑1 (MQ=255)
                                                                                                  cgATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTa                                                         >  1:685764/1‑99 (MQ=39)
                                                                                                  cgATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCaacaac                 >  2:769881/1‑139 (MQ=255)
                                                                                                       tAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTc            >  2:191830/1‑139 (MQ=255)
                                                                                                          aTAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAgg         <  2:155321/139‑1 (MQ=255)
                                                                                                          aTAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAgg         <  1:769881/139‑1 (MQ=255)
                                                                                                              cGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                             <  2:603943/51‑1 (MQ=255)
                                                                                                              cGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                             >  1:603943/1‑51 (MQ=255)
                                                                                                              cGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                  >  2:73489/1‑126 (MQ=255)
                                                                                                              cGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaacaa                  <  1:73489/126‑1 (MQ=255)
                                                                                                               gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      >  2:220002/1‑57 (MQ=255)
                                                                                                               gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      <  1:220002/57‑1 (MQ=255)
                                                                                                               gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                       >  2:594579/1‑72 (MQ=255)
                                                                                                               gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                       <  1:594579/72‑1 (MQ=255)
                                                                                                               gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGGGGCGTGAACGCCTTATCCGACCTACCCGCGAGGCATGATAAAACGCACCAACAACGCGTCAGGCTCgc    >  2:215356/1‑138 (MQ=39)
                                                                                                               gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGt    >  2:829160/1‑139 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      <  2:319824/55‑1 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      >  1:319824/1‑55 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGtt                                                                                 <  2:257346/60‑1 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGtt                                                                                 >  1:257346/1‑60 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTc            <  1:479754/129‑1 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTc            >  2:479754/1‑129 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCa           <  1:15862/130‑1 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCa           >  2:15862/1‑130 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg  >  2:364200/1‑139 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg  >  2:338028/1‑139 (MQ=255)
                                                                                                                 ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg  >  2:867745/1‑139 (MQ=255)
                                                                                                                                |                                                                                                                           
TCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAG  >  NC_000913/3736032‑3736282

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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