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
A1 F2 I225 R1 227 21.4 1179702 97.1% 1145490 86.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 2,819,095 T→C intergenic (‑160/‑96) mltB ← / → srlA lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,819,0950TC81.8% 16.5 / 0.0 11intergenic (‑160/‑96)mltB/srlAlytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (5/4);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01

CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAA  >  NZ_CP009273/2819012‑2819166
                                                                                   |                                                                       
cTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCAtttt                                                                   >  2:498924/1‑90 (MQ=255)
              cTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAac                                                     <  2:140850/90‑1 (MQ=255)
              cTTTACATAACTCAACTCATTCCCCTCGCTACCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAac                                                     <  1:483087/90‑1 (MQ=255)
                ttACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAacac                                                   >  2:12553/1‑90 (MQ=255)
                       actcaactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaaa                                            <  1:549920/90‑1 (MQ=255)
                          caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt                                         >  1:554259/1‑90 (MQ=255)
                                 ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc                                  >  2:426950/1‑90 (MQ=255)
                                      cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt                             >  1:170804/1‑90 (MQ=255)
                                      cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt                             >  1:27274/1‑90 (MQ=255)
                                                        aaaCTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTg           <  2:136120/90‑1 (MQ=255)
                                                                 aaTTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATaaaa  <  1:426950/90‑1 (MQ=255)
                                                                                   |                                                                       
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAA  >  NZ_CP009273/2819012‑2819166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCC  >  NZ_CP009273/2819026‑2819176
                                                                     |                                                                                 
CTTTACATAACTCAACTCATTCCCCTCGCTACCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAAT                                                     <  SRR3722109.490361/100‑1 (MQ=60)
  TTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCT                                                   >  SRR3722109.562682/1‑100 (MQ=60)
         ACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATC                                            <  SRR3722109.558274/100‑1 (MQ=60)
              ACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATT                                       >  SRR3722109.172916/1‑100 (MQ=60)
              ACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATT                                       >  SRR3722109.27610/1‑100 (MQ=60)
                                                   AATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCC  <  SRR3722109.433226/100‑1 (MQ=60)
                                                                     |                                                                                 
CTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCC  >  NZ_CP009273/2819026‑2819176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑