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
A7 F55 I1 R1 9 17.1 823558 91.9% 756849 140.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947 4,965,027 C→A E126* (GAA→TAA)  fleQ ← transcriptional regulator FleQ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,965,0270CA93.3% 38.9 / ‑3.0 15E126* (GAA→TAA) fleQtranscriptional regulator FleQ
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (7/7);  total (8/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01

GGATCAGCACGCTGGCGTCGGTATCCGCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTCGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAGGTCTTCCGGCAGCTCGGCGGAAGAAATTTCACCTAAAAGCAAAACCGGAAGGAACTCA  >  NC_002947/4964886‑4965172
                                                                                                                                             |                                                                                                                                                 
ggATCAGCACGCTGGCGTCGGTATCCGCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGa                                                                                                                                           >  2:271903/1‑150 (MQ=255)
     aGCACGCTGGCGTCGGTATCCGCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTgg                                                                                                                                      <  2:99024/150‑1 (MQ=255)
      gCACGCTGGCGTCGGTATCCGCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTggg                                                                                                                                     <  1:271903/150‑1 (MQ=255)
                   ggTATCCGCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTGGGCACGGTGCAGCGa                                                                                                                        <  1:170530/150‑1 (MQ=255)
                          gCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGc                                                                                                                 >  1:371856/1‑150 (MQ=255)
                                                                aCGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCGGGTTGGAAAg                                                                           >  1:65894/1‑150 (MQ=255)
                                                                            aaCCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTgg                                                                                                                                      <  1:114425/79‑1 (MQ=255)
                                                                            aaCCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTgg                                                                                                                                      >  2:114425/1‑79 (MQ=255)
                                                                                              aTTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTCGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAGGTCTTCCGGCAGCTc                                             >  2:359149/1‑150 (MQ=255)
                                                                                                    ttCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAgg                                                           <  1:371180/130‑1 (MQ=255)
                                                                                                    ttCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAgg                                                           >  2:371180/1‑130 (MQ=255)
                                                                                                               gACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTggg                                                                                                                                     <  1:17840/45‑1 (MQ=255)
                                                                                                               gACCCCGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTggg                                                                                                                                     >  2:17840/1‑45 (MQ=255)
                                                                                                                   ccGCTCGCGCGCCTGGTCATACATTTAGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAGGTCTTCCGGCAGCTCGGCGGACGAAATTTCCACTaa                        >  2:180400/1‑150 (MQ=255)
                                                                                                                                         aTTTAGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATGGGCTGTAGCTGGCCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAGGTCGTGCAGCAGCTCGGCGGAAGAAATTTCACCTAAAAGCAAAACCGGAAGGAACTCa  <  1:180400/150‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                                 
GGATCAGCACGCTGGCGTCGGTATCCGCCACTTGCTGCATCATCTGCCGCACGTGCTGAATGGCACGACTGGTGCCAACCAGGCTGCGGAACAGATTGGGTTCGCGCTGGCGACCCCGCTCGCGCGCCTGGTCATACATTTCGCGGTAGACCTGGGCACGGTGCAGCGAGTCCAGCAATTGGCTGTAGCTTGGCGGCATTTCCAGGTTGGAAAGCACCCGGCGGCGAAGGTCTTCCGGCAGCTCGGCGGAAGAAATTTCACCTAAAAGCAAAACCGGAAGGAACTCA  >  NC_002947/4964886‑4965172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A