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
A10 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 357,626 2 bp→TA intergenic (+172/+164) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,6260CT100.0% 43.3 / NA 16intergenic (+172/+165)codA/cynRcytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (8/8);  total (8/8)
*NC_000913357,6270CA100.0% 43.0 / NA 16intergenic (+173/+164)codA/cynRcytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (8/8);  total (8/8)

CAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCA  >  NC_000913/357558‑357756
                                                                    ||                                                                                                                                 
cAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGACTGTCTGCCAGCTGTAGTTTATGCCGGATgcggcg                                                              >  2:527594/1‑139 (MQ=17)
            gCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTAt                                                  >  2:830576/1‑139 (MQ=18)
                        tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGc                                             >  1:1313775/1‑132 (MQ=18)
                        tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGc                                             <  2:1313775/132‑1 (MQ=255)
                        tgtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTa                                      >  1:940365/1‑139 (MQ=18)
                             gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCa                                 >  2:901388/1‑139 (MQ=255)
                             gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCa                                 <  2:940365/139‑1 (MQ=21)
                                  tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGaa                            >  1:1591162/1‑139 (MQ=255)
                                        gATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTa                      <  1:830576/139‑1 (MQ=255)
                                           tcatttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGc                   <  1:513770/139‑1 (MQ=255)
                                           tcatttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGc                   >  2:513770/1‑139 (MQ=255)
                                                  cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGa                             >  1:110929/1‑122 (MQ=255)
                                                  cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGa                             <  2:110929/122‑1 (MQ=255)
                                                      aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGACTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGt        <  1:527594/139‑1 (MQ=255)
                                                            cgcgCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCa  <  2:1591162/139‑1 (MQ=255)
                                                              cgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTa                      <  1:1276181/117‑1 (MQ=255)
                                                                    ||                                                                                                                                 
CAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCA  >  NC_000913/357558‑357756

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A