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
A5 F13 I0 R1 213 60.4 2554362 98.6% 2518600 147.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 3,845,703:1 +G 100% intergenic (‑70/+28) PP_3394 ← / ← PP_3395 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC3,845,7031.G100.0% 39.2 / NA 12intergenic (‑70/+28)PP_3394/PP_33953‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (5/7);  total (5/7)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCAT  >  NC_002947_CJ‑RC/3845567‑3845820
                                                                                                                                         |                                                                                                                     
gCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGGCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCAt                                                                                                            <  2:112781/149‑1 (MQ=255)
 cATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATc                                                                                                           <  1:276064/149‑1 (MQ=255)
   tGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGt                                                                                                         <  6:306762/149‑1 (MQ=255)
     aTCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCa                                                                                                       <  4:146836/149‑1 (MQ=255)
      tCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAg                                                                                                      <  3:306964/149‑1 (MQ=255)
               ggCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATgg                                                                                             <  1:214481/149‑1 (MQ=255)
                      cAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGc                                                                                       <  3:66142/148‑1 (MQ=255)
                            aTCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCCCGAAGGGTCAGCCCCCGcc                                                                                >  6:164586/1‑149 (MQ=255)
                                 gcAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTTGTGCATGGGCCGGCCCGATGGGTAAGCCCGCGcccgggc                                                                           >  7:214940/1‑145 (MQ=255)
                                              attgattgTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCAGATACATAGTAAGCCACGATGGGTAAGCCCGCGCCCAGCCAGGCCGGTGCACg                                                              >  5:240400/1‑149 (MQ=255)
                                                   ttgttattgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCAGATCCATCGGCCGCCCCGCTGGGTAAGCCCCCGCCCGGCCAGGCCGGGGCACgcagc                                                          >  8:248909/1‑148 (MQ=255)
                                                                                                          cTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATACAAAGTCAGCCACCAAGGATAAGCCCCCGCCCAGCCAGGCCCGTGCACCCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCCCCAGCGAGAGCCGGTGCCGGTCGCGCAt  >  8:220858/1‑149 (MQ=255)
                                                                                                                                         |                                                                                                                     
GCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGCGCAT  >  NC_002947_CJ‑RC/3845567‑3845820

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