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
A35 F9 I0 R1 1164 192.0 7567036 97.0% 7340024 130.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 940,751 T→C 42.1% intergenic (+31/‑208) serS → / → dmsA seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913940,7510TC42.1% 6.2 / 20.3 19intergenic (+31/‑208)serS/dmsAseryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A
Reads supporting (aligned to +/- strand):  ref base T (5/6);  new base C (4/4);  total (9/10)
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

GGCTGTTGGTCGTACGCTGGTTGCAGTAATGGAAAACTATCAGCAGGCTGATGGTCGTATTGAAGTACCAGAAGTTCTGCGTCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGAT  >  NC_000913/940606‑940849
                                                                                                                                                 |                                                                                                  
ggCTGTTGGTCGTACGCTGGTTGCAGTAATGGAAAACTATCAGCAGGCTGATGGTCGTATTGAAGTACCAGAAGTTCTGCGTCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCCGca                                                                                                 >  2:993213/1‑148 (MQ=255)
          cGTACGCTGGTTGCAGTAATGGAAAACTATCAGCAGGCTGATGGTCGTATTGAAGTACCAGAAGTTCTGCGTCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCCGCAGGCGCttttt                                                                                       <  1:993213/149‑1 (MQ=255)
                                                                      gAAGTTCTGCGTCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGa                                                                         <  4:274737/103‑1 (MQ=255)
                                                                      gAAGTTCTGCGTCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGa                                                                         >  3:274737/1‑103 (MQ=255)
                                                                                 tCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCtttttt                                                                                      >  4:532115/1‑79 (MQ=255)
                                                                                 tCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCtttttt                                                                                      <  3:532115/79‑1 (MQ=255)
                                                                                       tatGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCtt                                                                            <  1:605543/83‑1 (MQ=255)
                                                                                       tatGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCtt                                                                            >  2:605543/1‑83 (MQ=255)
                                                                                        atGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCCGCAGGCGCtt                                                                                          <  2:641853/68‑1 (MQ=255)
                                                                                        atGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCCGCAGGCGCtt                                                                                          >  1:641853/1‑68 (MQ=255)
                                                                                               gACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGAt  <  4:1738615/149‑1 (MQ=255)
                                                                                                              gCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCt                 >  2:276466/1‑119 (MQ=255)
                                                                                                              gCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCt                 <  1:276466/119‑1 (MQ=255)
                                                                                                                       cAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCtt                                                                            <  3:1085950/51‑1 (MQ=255)
                                                                                                                       cAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCtt                                                                            >  4:1085950/1‑51 (MQ=255)
                                                                                                                                       aaaaaGCGCCCGCAGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCttt     <  1:1075709/106‑1 (MQ=255)
                                                                                                                                       aaaaaGCGCCCGCAGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCttt     >  2:1075709/1‑106 (MQ=255)
                                                                                                                                        aaaaGCGCCCGCAGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAAta                                     >  2:711305/1‑73 (MQ=38)
                                                                                                                                        aaaaGCGCCCGCAGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAAta                                     <  1:711305/73‑1 (MQ=255)
                                                                                                                                                 |                                                                                                  
GGCTGTTGGTCGTACGCTGGTTGCAGTAATGGAAAACTATCAGCAGGCTGATGGTCGTATTGAAGTACCAGAAGTTCTGCGTCCGTATATGAACGGACTGGAATATATTGGCTAATACCCAATTTTTCTGAATCTAAAAAGCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGATACCGAACAATAATTACTCCTCACTTACACGTAATACTACTTTCGAGTGAAAATCTACCTATCTCTTTGAT  >  NC_000913/940606‑940849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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