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
A29 F999 I0 R1 9 7.7 636200 44.2% 281200 128.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,188,282 G→A R978H (CGT→CAT)  rpoC → RNA polymerase subunit beta'

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,188,2820GA85.7% 11.8 / NA 7R978H (CGT→CAT) rpoCRNA polymerase subunit beta'
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (3/3);  minor base C (0/1);  total (3/4)
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

GAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAAC  >  NC_000913/4188188‑4188406
                                                                                              |                                                                                                                            
gAATCCAGCAACCCAAGGGAAAACAAAGGTGGCATCAAGCTCAGGAACGTGAAATCGGTTGGGAACTCCAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGt                                                                                            <  1:97509/129‑1 (MQ=255)
               tggAAAAACAAAGGGAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTAAACGCCAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGc                                                                             <  1:212352/127‑1 (MQ=255)
                  aaaaaCAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCTTCCTAAAGAAAGCTAc                                                                          >  1:263081/1‑129 (MQ=255)
                          aGGTAGCATCCAGCTCAGGAACGGGAAGGCGGTTGTGAACCCCAGCGGGAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTAcc                                                                  <  1:602985/129‑1 (MQ=255)
                                             aaggTGAAGGGGGTGGTGAAC‑CCAGGGGGAAAACGGTTTACCCTTCCCCAAAAACTGAACGTAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCGACAAAGTACCTTACGGTGCGGTACTGGCGa                                              <  1:159367/126‑1 (MQ=255)
                                                                                ggTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTAAAAAGTACCTTACGTTGCGGACCTGGCAAAAGGCGTTGGGGAA‑AGGTGTGTGGCGGGGAAAc            >  1:213970/1‑128 (MQ=255)
                                                                                         ttCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGAACTGGCGAAAGGCACTGGCGACCGGGTGCCTGAC‑GCGAAACCGTTGCAAAc  >  1:418485/1‑129 (MQ=255)
                                                                                              |                                                                                                                            
GAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAAC  >  NC_000913/4188188‑4188406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A