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
A4 F1 I1 R1 765 39.6 1867486 94.4% 1762906 108.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,286,859 T→C intergenic (+333/+207) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,286,8590TC100.0% 33.3 / NA 13intergenic (+333/+207)narI/rttRnitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/6);  total (7/6)

AGCTTCTCATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTC  >  NC_000913/1286811‑1286994
                                                |                                                                                                                                       
aGCTTCTCATCCTTACCCGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGc                                               <  2:54620/139‑1 (MQ=12)
               cccGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAg                                                                                                                <  1:531240/59‑1 (MQ=14)
               cccGCATGGGCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAg                                                                                                                >  2:531240/1‑59 (MQ=11)
                       ggCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCt                           <  1:108070/136‑1 (MQ=255)
                       ggCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCt                           >  2:108070/1‑136 (MQ=255)
                       ggCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGa                        >  1:591591/1‑139 (MQ=255)
                        gCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCggg                                                                                                                           <  1:320045/39‑1 (MQ=14)
                        gCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCggg                                                                                                                           >  2:320045/1‑39 (MQ=14)
                        gCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGc                                                                                                                         >  1:751399/1‑41 (MQ=255)
                        gCAGAATATTTGATTGCGGATTCGCTTGAGAATTCCGGGGc                                                                                                                         <  2:751399/41‑1 (MQ=255)
                                        cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCt                           >  1:814195/1‑119 (MQ=255)
                                        cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCt                           <  2:814195/119‑1 (MQ=255)
                                        cGGATTCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGTACCTTAATCGaa       >  1:727512/1‑139 (MQ=255)
                                             tCGCTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAATCGAAGCTtc  <  2:253198/139‑1 (MQ=255)
                                                |                                                                                                                                       
AGCTTCTCATCCTTCCCCGCTTGGGCAGAATATTTGATTGCGGATTCGTTTGAGAATTCCGGGGCTTTTGAAAGTGATGGTGGTGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGACGCTCGAGCCGAACCTTAGTCGAAGCTTC  >  NC_000913/1286811‑1286994

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A