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 F110 I2 R1 12 58.9 2036372 94.8% 1930480 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,938,656 Δ1 bp coding (1008/1443 nt) pykA → pyruvate kinase II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,938,6560C.97.6% 173.6 / ‑3.2 42coding (1008/1443 nt)pykApyruvate kinase II
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base . (20/21);  minor base G (1/0);  total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

ATTACTAACCCGATGCCGACGCGTGCAGAAGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCGCGTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGAAAGGCGTTACGGCGAT  >  NC_000913/1938519‑1938793
                                                                                                                                         |                                                                                                                                         
aTTACTAACCCGATGCCGACGCGTGCAGACGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCCGCCGAAACTGCCGCTGGGCAGTATCCGTCCGCAACCGTCGCAGCCATAGCGCGGGttgc                                                                                                                                      >  1:194684/1‑141 (MQ=255)
 ttcgtAATCCGAGGCCGAGCGGTGGAGAAGGCATGGAGGGAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACCGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGcc                                                                                                                                    <  1:73276/139‑1 (MQ=255)
     tAACCCGATGCCGACGCGTGCAGAAGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCCTGGCGCG‑GTTTGCCTggc                                                                                                                                >  1:1010456/1‑142 (MQ=255)
         ccGATGCCGACGCGGGCAGAAGTCATGGACGTGGCACACGCCGTGCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCg                                                                                                                            <  2:202949/143‑1 (MQ=255)
                cGACGCGTGCAGAAGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAGACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGaaaaaa                                                                                                                     <  2:334274/143‑1 (MQ=255)
                 gACGCGTGCAGAAGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCGGTCTGTAGTCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAAt                                                                                                                    >  2:325655/1‑143 (MQ=255)
                       tGCAGAAGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAg                                                                                                              >  1:691005/1‑143 (MQ=255)
                              gTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTTATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAAc                                                                                                       <  1:587649/143‑1 (MQ=255)
                                    gACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAGCTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCt                                                                                                 >  2:527689/1‑143 (MQ=255)
                                      cGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGCGCGGAACAAATCCCGAGCATCAACGTTTCtga                                                                                               >  1:1006775/1‑141 (MQ=255)
                                          gCAAACGCCCTTCTGGCTGGTACTGACGCTGTGATGCTGGCTGCAGAAACTGCCGCTGGGCAGTATCCGTTAGAAAGCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAacac                                                                                           <  2:141564/143‑1 (MQ=255)
                                            aaaCGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCGGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCg                                                                                         >  2:528132/1‑143 (MQ=255)
                                               cGCCGTTCTGGATGGTACTGGCGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCt                                                                                      <  1:940286/143‑1 (MQ=255)
                                                gCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGCGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGAGGAAAAAATCCCGAGCATCAACGTTTCTAAACAGCGtgtg                                                                                     >  1:410595/1‑143 (MQ=255)
                                                    ttCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACg                                                                                 >  2:568233/1‑143 (MQ=255)
                                                        ggATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCa                                                                             <  2:795464/143‑1 (MQ=255)
                                                           tcgTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGtt                                                                          <  2:152867/141‑1 (MQ=255)
                                                              tACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCAGCAACGTTACTAAACACCGTCTGGACGTTCAGGTCGa                                                                       >  2:303350/1‑143 (MQ=255)
                                                              tACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GGTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTCAACCCCGTCAGGACGTTCAGTTCGa                                                                       >  1:271053/1‑143 (MQ=255)
                                                                   aCGCGGTGATGCTGGCTGCAGGAACTGCCGCGGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAAtg                                                                  <  1:635062/143‑1 (MQ=255)
                                                                                  cggCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGCAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTg                                                   <  2:351041/141‑1 (MQ=255)
                                                                                  cTGCAGAAGCGGCCGCTGGGCAGTAGCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCGTGGGTGCGGAACAAACTCGGATCATCAACGTTTCGAAACACCGTCTGGACGGTCAGTTCGACAATGTGGAAGAAGCTATTg                                                   <  1:167937/143‑1 (MQ=255)
                                                                                   tGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTCTTGc                                                  >  1:799947/1‑143 (MQ=255)
                                                                                   tGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGc                                                  <  1:528132/143‑1 (MQ=255)
                                                                                       gAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCaag                                              >  2:789544/1‑141 (MQ=255)
                                                                                              ccGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAACAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGGCAGGTCAGCaa                                       >  1:195664/1‑143 (MQ=255)
                                                                                               cGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAAt                                      >  2:871610/1‑143 (MQ=255)
                                                                                                 cTGGGCAGTATCCGACAGAAACCCTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAACAATCCCGAGCATCAACGTTTCTGAGCACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCCATTGCCATGTCAGCagcgt                                    >  1:537868/1‑139 (MQ=255)
                                                                                                   gggCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTAc                                  >  2:858059/1‑143 (MQ=255)
                                                                                                   gggCAGTATCCGTCAGAAACCGTGGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTAc                                  <  2:526064/143‑1 (MQ=255)
                                                                                                    ggCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACg                                 <  2:127821/143‑1 (MQ=255)
                                                                                                      cAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGCAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCACTGTACGCa                               >  1:883137/1‑143 (MQ=255)
                                                                                                           tCCGTCAGAAACCGTTGCAGCCATCGCGCG‑GTTTGCCTTGTTTCTGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTaa                          <  2:764697/143‑1 (MQ=255)
                                                                                                              gtgaGAAAGCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAacca                       <  2:1005969/140‑1 (MQ=255)
                                                                                                              gTCAGAAACCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAacca                       >  2:946473/1‑143 (MQ=255)
                                                                                                                   aaaCCGTGGCAGCCATGGCGCG‑GTTGGCCGGGGTGCGGAAGAAATCCCGAGCATCACCGTTTCTAAACACCGTCTGGCCGTTCAGTCCGACAATGTGGAAGCAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGa                  <  1:916732/143‑1 (MQ=255)
                                                                                                                     aCCGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAAACCCGAGCCTCAATGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGaaa                <  2:847843/143‑1 (MQ=255)
                                                                                                                       cggtggaGCCGTGGCGCG‑GTTGACGTGGGGGCGGAAGAGATCCCGAGCATCAACGTTTCTAGACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGTTAACCACCTGAAAgg              <  1:856987/137‑1 (MQ=255)
                                                                                                                       cGTTGCAGCCATGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGAAAgg              >  2:941141/1‑143 (MQ=255)
                                                                                                                        gtgggatgcATGGCGCG‑GGTTGCGTGGCTGCGGAAAACATCCCGAGCATCAACGGATCTAAACAGCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGAAAGGc             <  2:294907/135‑1 (MQ=255)
                                                                                                                                 aTGGCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCGTGAACGATTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGCAAGGCATTACGGCg    >  1:517796/1‑143 (MQ=255)
                                                                                                                                   ggCGCG‑GTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGAAAGGCGTTACGGCGat  <  2:664445/143‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                         
ATTACTAACCCGATGCCGACGCGTGCAGAAGTCATGGACGTAGCAAACGCCGTTCTGGATGGTACTGACGCTGTGATGCTGTCTGCAGAAACTGCCGCTGGGCAGTATCCGTCAGAAACCGTTGCAGCCATGGCGCGCGTTTGCCTGGGTGCGGAAAAAATCCCGAGCATCAACGTTTCTAAACACCGTCTGGACGTTCAGTTCGACAATGTGGAAGAAGCTATTGCCATGTCAGCAATGTACGCAGCTAACCACCTGAAAGGCGTTACGGCGAT  >  NC_000913/1938519‑1938793

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A