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
A10 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,756,750 A→T K351N (AAA→AAT)  pykF → pyruvate kinase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,756,7500AT97.8% 145.9 / ‑3.5 46K351N (AAA→AAT) pykFpyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (21/24);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.69e-01

CTGACGCAGTGATGCTGTCTGGTGAATCCGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAAACTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCGGTAAATCTGCTCGCGCAGTACGTAAATACTTCCCGGATGCCACCATC  >  NC_000913/1756614‑1756885
                                                                                                                                        |                                                                                                                                       
cTGACGCAGTGATGCTGTCTGGTGAATCCGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCt                                                                                                                                       >  2:614061/1‑139 (MQ=255)
     gCAGTGATGCTGTCTGGTGAATCCGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCa                                                                                                                                  >  1:828709/1‑139 (MQ=255)
        gTGATGCTGTCTGGTGAATCCGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTa                                                                                                                               >  2:1439659/1‑139 (MQ=255)
             gCTGTCTGGTGAATCCGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGaa                                                                                                                          <  1:614061/139‑1 (MQ=255)
                            cGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCgtggt                                                                                                           <  2:828709/139‑1 (MQ=255)
                            cGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCgtggt                                                                                                           <  2:701640/139‑1 (MQ=255)
                                             cGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTgcg                                                                                                                                    >  1:914116/1‑97 (MQ=255)
                                             cGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTgcg                                                                                                                                    <  2:914116/97‑1 (MQ=255)
                                             cGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATg                                                                                                                  >  2:1150351/1‑115 (MQ=255)
                                             cGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATg                                                                                                                  <  1:1150351/115‑1 (MQ=255)
                                              gCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGaa                                                                                         >  2:1021929/1‑139 (MQ=255)
                                                   aaGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACt                                                                                    <  2:749271/139‑1 (MQ=255)
                                                        gTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATg                                                                               <  1:1021929/139‑1 (MQ=255)
                                                            cTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTcc                                                                           >  2:1219398/1‑139 (MQ=255)
                                                                cATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTg                                                                       >  2:428866/1‑139 (MQ=255)
                                                                   ggCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAAc                                                                                                <  1:803716/111‑1 (MQ=255)
                                                                   ggCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAAc                                                                                                >  2:803716/1‑111 (MQ=255)
                                                                     cGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGt                                                                  <  1:1219398/139‑1 (MQ=255)
                                                                       aCCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAg                                                                                                                         >  2:800202/1‑82 (MQ=255)
                                                                       aCCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAg                                                                                                                         <  1:800202/82‑1 (MQ=255)
                                                                          aTCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTg                                                             <  1:1237270/139‑1 (MQ=255)
                                                                                     tACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGc                                                  <  1:428866/139‑1 (MQ=255)
                                                                                     tACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGc                                                  >  1:1290345/1‑139 (MQ=255)
                                                                                      accgaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAGCt                                                                                    <  1:88594/104‑1 (MQ=255)
                                                                                      accgaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACt                                                                                    >  2:88594/1‑104 (MQ=255)
                                                                                      accgaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAg                                                     >  1:1133902/1‑135 (MQ=255)
                                                                                      accgaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAg                                                     <  2:1133902/135‑1 (MQ=255)
                                                                                      accgaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAAACTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCg                                                 >  2:1433614/1‑139 (MQ=255)
                                                                                         gaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGc                                                                              <  1:781744/107‑1 (MQ=255)
                                                                                         gaccgCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGc                                                                              >  2:781744/1‑107 (MQ=255)
                                                                                               gTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCg                                                                                                               <  1:836211/68‑1 (MQ=255)
                                                                                               gTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCg                                                                                                               >  2:836211/1‑68 (MQ=255)
                                                                                                tgatgaACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGa                                                                      >  2:934125/1‑108 (MQ=255)
                                                                                                tgatgaACAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGa                                                                      <  1:934125/108‑1 (MQ=255)
                                                                                                     aaCAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCGGTAAATCTGCTcgcg                                  <  1:1439659/139‑1 (MQ=255)
                                                                                                       cAGCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCGGTAAATCTGCTCGCGCa                                <  1:1504315/139‑1 (MQ=255)
                                                                                                         gCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTgg                                                                >  2:324225/1‑105 (MQ=255)
                                                                                                         gCCGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTgg                                                                <  1:324225/105‑1 (MQ=255)
                                                                                                           cGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGt                                                                  >  2:905308/1‑101 (MQ=255)
                                                                                                           cGTCTCGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGt                                                                  <  1:905308/101‑1 (MQ=255)
                                                                                                             tctcGAGTTCAACAATGACAACCGTAATCTGCGCATTACCg                                                                                                                            >  2:75119/1‑41 (MQ=255)
                                                                                                             tctcGAGTTCAACAATGACAACCGTAATCTGCGCATTACCg                                                                                                                            <  1:75119/41‑1 (MQ=255)
                                                                                                             tctcGAGTTCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCGGTAAATCTGCTCGCGCAGTACGt                          >  1:730836/1‑139 (MQ=255)
                                                                                                                    ttCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGa                                                                                                   <  2:1348659/59‑1 (MQ=255)
                                                                                                                    ttCAACAATGACAACCGTAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGa                                                                                                   >  1:1348659/1‑59 (MQ=255)
                                                                                                                                     tAATCTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCGGTAAATCTGCTCGCGCAGTACGTAAATACTTCCCGGATGCCACCATc  <  2:1290345/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                       
CTGACGCAGTGATGCTGTCTGGTGAATCCGCAAAAGGTAAATACCCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAACAGCCGTCTCGAGTTCAACAATGACAACCGTAAACTGCGCATTACCGAAGCGGTATGCCGTGGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGCGGTAAATCTGCTCGCGCAGTACGTAAATACTTCCCGGATGCCACCATC  >  NC_000913/1756614‑1756885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A