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
A11 F20 I0 R1 35 38.1 1546666 86.7% 1340959 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,159,147 C→G 16.9% R220G (CGC→GGC)  oxyR → DNA‑binding transcriptional dual regulator OxyR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,159,1470CG16.9% 88.6 / 9.6 45R220G (CGC→GGC) oxyRDNA‑binding transcriptional dual regulator OxyR
Reads supporting (aligned to +/- strand):  ref base C (19/18);  new base G (2/6);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 2.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

TCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCACG  >  NC_000913/4159005‑4159283
                                                                                                                                              |                                                                                                                                        
tCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCTTATCTGGCAGGTGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTcc                                                                                                                                          <  1:178998/143‑1 (MQ=255)
      gTGGGCGGACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGa                                                                                                                                    <  2:483009/143‑1 (MQ=255)
          gCGAGCCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAGCTGCTGATGCTGGAAGATGGTCACTGGTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAg                                                                                                                                <  2:757951/143‑1 (MQ=255)
          gCGAACCGCGAATGCGTATCGATGGTCGTTCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAg                                                                                                                                <  1:629968/143‑1 (MQ=255)
            gAACCGCGAATGCGTAACGATGGCCGATCTGGCAGGGGCAACACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCCATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACCCACTCCCGCGCGACCAgac                                                                                                                              >  1:543611/1‑141 (MQ=255)
                cgcgAATGCTTACCGATGGCCGATCTGGCAGGGGAAAAACGGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGa                                                                                                                          <  1:89339/143‑1 (MQ=255)
                cgcgAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGa                                                                                                                          >  1:253382/1‑143 (MQ=255)
                  cggaTGCGTACCGATGGCCGATCTCGCAGCGGAAATACCGCTGATGCTCTAAGATTGTTACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGCAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGaaa                                                                                                                        <  2:28352/140‑1 (MQ=255)
                  cgAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGGCACTGTTTGCGCGATCAGGCAATGGGTTTCTGGTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGaaa                                                                                                                        <  1:534159/143‑1 (MQ=255)
                        tgTACCGTTTGTCGATCTGGCAGGGGAAAAATTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCGGCGCGACCAGCCTGGAAACTCTgc                                                                                                                  <  1:430257/142‑1 (MQ=255)
                            ccGATGGTCGATCTGGTAGGGTATAAACTTCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCaa                                                                                                              <  1:228588/143‑1 (MQ=255)
                                           gCAGGGGAAAAGCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGTTCGTTCACTTTGCATCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAgg                                                                                               <  1:557819/143‑1 (MQ=255)
                                           gCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACTCTTCCGCGCGACCAGCCTGGAGTCTCTGCGCTATCTGGTGGGGGCAgg                                                                                               >  1:244950/1‑143 (MQ=255)
                                           gCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGAGCAACATGGTAGCGGCAgg                                                                                               >  1:32387/1‑143 (MQ=255)
                                             aGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAGACTCTGCGCAACATGGTGGCGGCAGGTa                                                                                             >  2:386701/1‑143 (MQ=255)
                                                 gAAAAACTGCTGATGCTGGAAGATGGTCACTATTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGAGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCgg                                                                                         >  2:227871/1‑143 (MQ=255)
                                                 gAAAAACTGCTGATGCTGGAAGATGGTCACTATTTGCACAATCAGGCAATGGGTTTCTGCTTTGAAGCCGGGGCGGATGAACATACACACTTCCGCGAGAACAGCCTGGAAACTCTGCGCAACATGGTGGTGGCAGGAAGCgg                                                                                         >  2:228161/1‑143 (MQ=255)
                                                  aaaaaCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACACGATAGCGGCAGGGAGCggg                                                                                        >  2:486142/1‑143 (MQ=255)
                                                        tgctgATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGCAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACt                                                                                  >  1:676357/1‑143 (MQ=255)
                                                             aTGCTGGAAGATGGTCACTGTTGGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACt                                                                             <  1:627092/143‑1 (MQ=255)
                                                                cTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTGTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGGAGGTAGCGGGGTCGTTTTACTGcc                                                                          >  1:55224/1‑143 (MQ=255)
                                                                 tgtaaGTTGGTAACTGGTGGCGCGGTTATGCTATGGGTTTCTTTTTTGAAGCCGGGTCTGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCa                                                                         <  2:613292/140‑1 (MQ=255)
                                                                 tGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTGTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCa                                                                         >  2:284613/1‑143 (MQ=255)
                                                                  ggAATATGGGCGCTGTTTGCACGATCAGGCGACGGGGTTCTGTGTTGAAGTCGGGGCGGAGTAAGCTACACAGTTCCGCGCGACCAGCCTGGGAACTGTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAg                                                                        <  2:239022/143‑1 (MQ=255)
                                                                  ggAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCCCTTTACTGCCAg                                                                        >  1:701600/1‑143 (MQ=255)
                                                                         ggTCCCTCTTTGCTCTATCACGCAATGGGTTTCTCTTTTGAAGCCGGGGCGGATGAAGATACACACTTCGGCGCTACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCgctggc                                                                 <  2:446564/143‑1 (MQ=255)
                                                                         ggTCACTGTGTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCGGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCgctggc                                                                 <  2:599697/143‑1 (MQ=255)
                                                                           tcccTGTCTGCGCGATCAGGCAATGGGTTGCTGTTTTGAACCCGGGGCGGATGAAGATACACCCTTCGGCGCGACCAGCCTGGATACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCgctggctg                                                               <  2:472711/140‑1 (MQ=255)
                                                                                  tggcgcGATCAGGCAATGGGTTTCTGTGTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTCGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTgccgcc                                                        <  1:735469/141‑1 (MQ=255)
                                                                                   tGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCGGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGccgccg                                                       >  1:218112/1‑143 (MQ=255)
                                                                                       cgATCTGGCAATGGGTTTCTGTTTTGAAGCCGGGGTGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAgc                                                   <  2:148488/143‑1 (MQ=255)
                                                                                         aTCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCCGGTAGCGGGATCACTTCACTGCCAGCGCTCGCTGTGCCGCCGGAgcgc                                                 >  2:725528/1‑143 (MQ=255)
                                                                                            aGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCaaa                                              <  1:503228/143‑1 (MQ=255)
                                                                                                 aTGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGAGCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGa                                         >  2:349315/1‑143 (MQ=255)
                                                                                                                gAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCAATGGGGATGATTAACt                          >  1:718156/1‑143 (MQ=255)
                                                                                                                  aGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGCGCGCAAACCCGGTGGGGTTGATTATGTGc                        >  2:575301/1‑143 (MQ=255)
                                                                                                                    ccGGGGCGGATGAAGATACACACTTCGGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGCTGTCTATCTGCCg                      >  2:142689/1‑143 (MQ=255)
                                                                                                                           tgATGCATATACACTCTTTCGCGCGACCAGCTTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTa               <  1:458619/142‑1 (MQ=255)
                                                                                                                           ggATGAAGATACCAACTTCCGCGCTACCAGTCTGGAAACTCTCCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCTAGCGCTGGTTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTa               <  2:94468/143‑1 (MQ=255)
                                                                                                                              tGAAGTTACACACTGTGGGGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTGCTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGc            <  2:382559/143‑1 (MQ=255)
                                                                                                                               gAATATACACACTTTGGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGcc           <  1:408033/143‑1 (MQ=255)
                                                                                                                                  gATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCGGCCGTGCATTAAGCCGGa        >  2:457594/1‑143 (MQ=255)
                                                                                                                                   ctgcactcTTCCGCGCGTCCAGCCTGGACTCTCTGCGCAACATGGTGGCGGCAGGTAGCGTTATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGaa       <  2:96589/140‑1 (MQ=255)
                                                                                                                                       acacTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTAGCGACAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGACGCCGGAGCGCAAACGCGAAGGAGTTGTTTATCTGCCGTGCATTAAACCGGAAacac   >  2:7551/1‑143 (MQ=255)
                                                                                                                                        cgcgtCCGCGCGACCAGCCTGGACACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCTATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCAct  <  2:150580/139‑2 (MQ=255)
                                                                                                                                        cacTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCAcg  >  1:489900/1‑143 (MQ=255)
                                                                                                                                              |                                                                                                                                        
TCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGCCAGCGCTGGCTGTGCCGCCGGAGCGCAAACGCGATGGGGTTGTTTATCTGCCGTGCATTAAGCCGGAACCACG  >  NC_000913/4159005‑4159283

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A