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
A3 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 3,791,606 T→G 26.1% D571A (GAC→GCC)  PP_3354 ← acyl‑CoA dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC3,791,6060TG26.1% 39.1 / 2.9 26D571A (GAC→GCC) PP_3354acyl‑CoA dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (12/7);  new base G (4/3);  total (16/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAAAGGCGGCTCGCACCTGTGTTCGGCGGACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTGGATGCAGCGCGCGCTGCGGGCCCAGGCGAAGGCCTGCAG  >  NC_002947_CJ‑RC/3791461‑3791751
                                                                                                                                                 |                                                                                                                                                 
tCAAAGGCGGCTCGCACCTGTGTTCGGCGGACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGa                                                                                                                                                <  3:55592/149‑1 (MQ=255)
    aGGCGGCTCGCACCTGTGTTCGGCGGACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATgg                                                                                                                                             >  6:232571/1‑148 (MQ=255)
          cTCGCACCTGTGTTCGGCGGACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCa                                                                                                                                       <  5:133063/148‑1 (MQ=255)
                   ctgtTCGGCGGACCGCAGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGCGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCCCGTCGATGGCCGCCACCTGCCgg                                                                                                                               >  6:380023/2‑147 (MQ=255)
                      ttCGGCGGACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAg                                                                                                                          <  2:10115/149‑1 (MQ=255)
                          gcggACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCg                                                                                                                      <  2:298111/149‑1 (MQ=255)
                          gcggACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCg                                                                                                                      >  4:114616/1‑149 (MQ=255)
                          gcggACCGCTGCATGCGCTACCGCCCCTCGCCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGCCAATTAATGGCAACGGCGTGGCGGCCGCGGCTATGGCCGCCACCTGCCGGTCGAGGTc                                                                                                                       <  5:232571/148‑1 (MQ=255)
                              aCCGCTGCATGCGCTACCGCCCCTCGGCTCGCCAGCCGCTGCCGGTGTTAATTACGACCTCGCACGTGGGTTTCATAACGATTCGGCAATTAATGGCAACGGCGTGGCGGCCGCGGCGATGGCCGCCACCTGCCGGTCGAGGTCGGgc                                                                                                                   <  6:347812/148‑1 (MQ=255)
                                            tACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGGCGAAGGCCCCCCCCAGCCCGGCGAGGGCGGGCCGCCGGGAGCCGAgg                                                                                                    >  2:363277/1‑149 (MQ=255)
                                               cGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGGCGATGGCCGCCCCCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAgg                                                                                                    >  3:137118/1‑146 (MQ=255)
                                               cGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGGCGATGGCCGCCACCAGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAgg                                                                                                    >  1:231489/1‑146 (MQ=255)
                                                                   gcagccgGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACCCTTTCCTGCtt                                                                             >  2:222550/1‑149 (MQ=255)
                                                                        ctgtgtTCATGACGACCTCGAACGTGGGTTTCATACCGATTCGGCAATGAATGGCAACGGCGGGGCGGCGGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTcc                                                                         <  8:148840/146‑1 (MQ=255)
                                                                             ttCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGgcg                                                                    <  6:398674/148‑1 (MQ=255)
                                                                                aTGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCCCCTGCCGGGCGCGGGCGGGCAGCCGGTAGCCGAGGGACCACCCAACGCTTTGCTGGTTTTACCGGCGCAgc                                                                >  4:336628/1‑149 (MQ=255)
                                                                                 tGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCGTTCCTGCTTTTACCGGCGCTgcg                                                               >  2:170336/1‑149 (MQ=255)
                                                                                           gCACGGGGGTTTCTTACCGATTCGGCAATTATTGGCAAGGGCGTGGGGGCGGGGTCGTTGGCCGCCACCTGCGGGTCGTGGTCGGGATGCTGGTTGCCGAGTAAGAACCAAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCa                                                      <  2:231489/148‑1 (MQ=255)
                                                                                                    tttCAGAACGATTCGACAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCAGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCAGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACg                                             >  8:284354/1‑148 (MQ=255)
                                                                                                        ttaaCTATTCGGAAATTAAGGGCAACGGGGGGGGGGCGGCGGCTATGCCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTg                                         <  5:19041/146‑1 (MQ=255)
                                                                                                         gAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGGCGATGGCCCCCACCTGCCGGTCGAGGTCGGGCAGCAGGGAGCCGAGGAAGAACCCAACGCGTTCCTGCTTTTACCGGCGCGGCGCCCCCCCCACAGGCAAccccgg                                         >  6:26317/1‑145 (MQ=255)
                                                                                                              aTTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCAGCGCCGCCCCCCCTGGCAACGCCGGGAtt                                     >  6:141761/1‑145 (MQ=255)
                                                                                                                           tgGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTGGATTCAGCGCGCGCAGCgg                      >  6:87670/1‑148 (MQ=255)
                                                                                                                                           gcCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTGGATGCAGCGCGCGCTGCGGGCCCAGGCGAAGGCCTg     >  2:114651/1‑149 (MQ=255)
                                                                                                                                              gcgTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTGGATGCAGCGCGCGCTGCGGGCCCAGGCGAAGGCCTgcag  >  4:42694/1‑149 (MQ=255)
                                                                                                                                               cgTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTGGATGCAGCGCGCGCTGCGGGCCCAGGCGAAGGCCTgcag  >  8:282442/1‑148 (MQ=255)
                                                                                                                                                 |                                                                                                                                                 
TCAAAGGCGGCTCGCACCTGTGTTCGGCGGACCGCTGCATGCGCTACCGCCCCTCGGCACGCCAGCCGCAGCCGGTGTTCATGACGACCTCGCACGTGGGTTTCAGAACGATTCGGCAATGAATGGCAACGGCGTGGCGGCCGCGTCGATGGCCGCCACCTGCCGGTCGAGGTCGGGCAGCAGGTAGCCGAGGAAGAACCCAACGCTTTCCTGCTTTTCCCGGCGCTGCGCCGCCCCCACTGGCAACGCCTGGATGCAGCGCGCGCTGCGGGCCCAGGCGAAGGCCTGCAG  >  NC_002947_CJ‑RC/3791461‑3791751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A