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
A4 F9 I0 R1 260 102.5 2178490 93.2% 2030352 226.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,708,844 C→G 20.7% A642A (GCC→GCG)  rsxC → SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,708,8440CG20.7% 38.4 / 4.3 28A642A (GCC→GCG) rsxCSoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex
Reads supporting (aligned to +/- strand):  ref base C (13/7);  new base G (3/3);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 6.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

CGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCG‑GCAGTTGC  >  NC_000913/1708611‑1709077
                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                           
cccgcCAAAGCCGGCAAGCTGGAACAGCAACAGGCTAAGGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTTGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGc                                                                                                                                                                                                                                         <  1:892903/236‑1 (MQ=255)
  cgcCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCATAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTTCCCGTGCAAAAGCCCGCAAGCTGGAACAGCAACAGGCTAATGCAGacacac                                                                                                                                                                                                                                      >  1:881257/1‑234 (MQ=255)
      aagagcgccaaacgggAGCAGCTACAGGCACATGCGAGACCAGAGAGCGAGGTGGACCGGCGAAAAGCGGCCCGCGAGGCAGCTAGGCCCCGGGCCCAAGCGCCCAAGCGGGAACAGCAGCCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCGGCCGTCGAAGCGGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACC‑AGaaga                                                                                                                                                                                                                                 <  2:200542/225‑3 (MQ=9)
                    gaaaCAGCAAAAGGCAAAGGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGGGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAAGGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCcg                                                                                                                                                                                                                    <  1:1013499/236‑1 (MQ=255)
                           cAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACACAAGGACGATCCGCGCAAAGCCGCCGTAGAAGCGGCTTATGCCCAAGCCAAAGCGCCCAAGCGGTAACCACACCCGGCGAATGGGGAGCCAACAACACCAGG‑CGATcccgaaccagt                                                                                                                                                                                                            >  2:776749/1‑230 (MQ=14)
                           cAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAACCCGCTATTGCCCGAGCCAAAGCACGCAAGCTGGAACATCAACACGCTAATGCCGAGCC‑AGAACAACAGGACGATCCCCGCaaac                                                                                                                                                                                                             >  1:254408/1‑237 (MQ=255)
                                                                       aGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCCCGCAAACGGGAACAACAACCGCCTAATGCGGAGCC‑AGAAGAACAGGGGGATCCGCGCAAAGCGGACGGCGAAGCGGCAATGGACCGGCCCaaaaaaacaaaaggag                                                                                                                                                                >  2:588423/1‑226 (MQ=14)
                                                                            ccgTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCCCCCAAACggggaaa                                                                                                                                                            >  1:608284/1‑234 (MQ=255)
                                                                                         tATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCGGGAACAGCACCAGGCTAACACCGAGCC‑AGAAGAACAGGTCGATCCCCGCAAACCCGCCGCCCAACCCGCTATTTTCCGCCCCCAAGCCCCCAAACGGGCACACCAACAggggaaaa                                                                                                                                              >  2:869256/1‑233 (MQ=11)
                                                                                                  tGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGGGCAAAGCCGCCGTCCAACCCGCTATTTCCCGCGCCAAACCGCGCAACCGGGAACAGCAACCGGCTAATGCGGAGccca                                                                                                                                     >  1:1015654/1‑237 (MQ=14)
                                                                                                  tGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAAGAACAGGTTGATCCGCGCAAACCCCCCGTCGAACCGGCTATTGCCCACGCCAAAGACCGCAAAAGGGAAAAGaaaaagggcaaaagggaggaga                                                                                                                                     >  2:466046/1‑220 (MQ=11)
                                                                                                      aaaGGGCGCAAGCTGGAAAAGCACAAGGCTAATGCGGAACCAGAAGACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCagaaga                                                                                                                                 <  1:769937/239‑1 (MQ=255)
                                                                                                           gggcAAGGTGGAACGGCAACCGGCCAAGGCGGAACCAGAAGAACAGGCCGACCCGCACAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAgg                                                                                                                            <  1:834807/237‑1 (MQ=14)
                                                                                                                                                     aCAGGGCGACCCGCGCAAAGCCGCGGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCC‑AGAACACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCAcg                                                                                    <  1:872787/237‑1 (MQ=255)
                                                                                                                                                         gTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGCGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGCAGCCGCTATTGCCCGCGCCAAAGCACGCAAACTGGCACAGCAACCGGCTAATCCGGAGCCAGAAGAACCAGGTGATCCGCCAAAACCCGCCGTcacagagcaacttgccacacacaa                                                                              >  2:1088794/1‑216 (MQ=11)
                                                                                                                                                              tCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTGATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGCCCGAGCCAAAGCCGGCAAACGGGAAAAGCAACCGGTTAATGCCGAGCCGGAAGAACAGGATAGTCCGCCCAAACGGGCGGTCAAAGCGGCAACTGCCCGCCCCAAAGAAc                                                                         >  2:436231/1‑239 (MQ=14)
                                                                                                                                                              tCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAAGCCGGAACCAGAAGAACAGGTTGATCCCCGCAAAGCTGCCGTCGAAGCGGCAATTGCACGCGCCAAGGccc                                                                         >  1:546885/1‑237 (MQ=255)
                                                                                                                                                                  cgcAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAACCAGAAGAACAGGTTGATCCGCGCAAAGCGCCCGTCGAACCGGCCATTGCACGCGcccaggccccaaa                                                                     >  1:1017281/1‑228 (MQ=17)
                                                                                                                                                                                             gCCCGTGCAAAAGCGCGCAAGCGGGAACAGCAACAGGTAAATGCGGAGCC‑AGAACACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGt                                          <  1:764141/239‑1 (MQ=255)
                                                                                                                                                                                                   tccAAAGAACCGAAGCTTGAACAGCAACGGGGTAATGCCGAGCC‑AAAAAAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGTTATTGCCCGAGCCAAAGCGCCCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCag                                     <  1:776749/237‑1 (MQ=17)
                                                                                                                                                                                                   gCCAAAGGCCTCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCag                                     <  1:656248/238‑1 (MQ=255)
                                                                                                                                                                                                      aaaccccccAAACTGGAACAGCAACAGGCTAATGCAAACCA‑AGAGCACGAGGCCGAGCCGCGAAAAGGCGACTACGAAGCGGATATTGCACGAGCCAAAGCCCGCAAGCGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCagaaga                                 <  2:1015654/231‑1 (MQ=14)
                                                                                                                                                                                                             gCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAACCTGGACCAGCAACAGGCTAATGCGGTACCAGAAGAAACGGtt                          >  1:352676/1‑239 (MQ=255)
                                                                                                                                                                                                                           cAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCCAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGAAGGCAAGACGGAAAAAACACAGGCTCAAGGGGAGCACGAAGAACAGGGTGaacggggccaaga            >  2:858920/1‑227 (MQ=14)
                                                                                                                                                                                                                               aGGCTAATGCCGGGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCCCGCAAACGGGCACAGCAACCGGCTAATGCGGAGCCAGAAGAACCGGTTGATCCGCGCAAAGCAGCCGCGGGAGCGGCTAGTGCACGCGGCCAATCCCCCAAGCTAGAAAGGCAAAAAGCTAAAGAGGGACAAGAAAAAAAgggagaaaacggacagaaggaa        >  2:570892/1‑219 (MQ=9)
                                                                                                                                                                                                                                     aTGCGGAACC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCGGCCGTCGACGCCGCTATTGCCCGCGCCCAAGCACGAAAGACGGACCAGAAAAAGGCTAATCCGCAGCCAGCAGAACAGGCGGATACCCGCCAACCG‑GCAggcga  >  2:293334/1‑234 (MQ=11)
                                                                                                                                                                                                                                     aTGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGCAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGGACAGCAACAAGCTAAAGCGGGACCCAAAGAACAGGCTGAACCGCGCAAAGCGCGCGGTTGc  >  2:647236/1‑239 (MQ=17)
                                                                                                                                                                                                                                      tGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAg                                                                                                                                                                            <  1:148257/68‑1 (MQ=255)
                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                           
CGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCG‑GCAGTTGC  >  NC_000913/1708611‑1709077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A