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 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 488,806 Δ1 bp 100% coding (3047/3363 nt) kefA → fused mechanosensitive channel proteins

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb488,8060A.77.8% 59.9 / 22.5 27coding (3047/3363 nt)kefAfused mechanosensitive channel proteins
Reads supporting (aligned to +/- strand):  ref base A (4/2);  new base . (8/13);  total (12/15)
Fisher's exact test for biased strand distribution p-value = 3.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

TTGACTGACACTACTACGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGAAAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGTGATGCACGAACCAATG  >  W3110S.gb/488745‑488870
                                                             |                                                                
ttGACTGACACTACTACGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGt                                                        <  1:1658504/71‑1 (MQ=255)
  gactgacACTACTACGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGAAAAAGTGCg                                                         >  1:2789525/1‑69 (MQ=255)
  gactgacACTACTACGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGAAAAAGTGCGt                                                        >  1:303991/1‑70 (MQ=255)
  gactgacACTACTACGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTa                                                       >  1:154000/1‑70 (MQ=255)
          ctactaCGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGtt                                                <  1:2734158/69‑1 (MQ=255)
              tacGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGaaaa                                                               <  1:1761602/51‑1 (MQ=255)
              tacGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGaa                                                                 <  1:443460/49‑1 (MQ=255)
              tacGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGaa                                                                 <  1:42400/49‑1 (MQ=255)
              tacGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGaa                                                                 <  1:2196732/49‑1 (MQ=255)
                cgcgTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAGGTGCGTAAAGTGTTACTGaa                                          <  1:985858/69‑1 (MQ=255)
                 gcgTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAggc                                       <  1:2316147/71‑1 (MQ=255)
                        gTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGAAAAAGTGCGTAAAGTGTTACTGAAGgcggcg                                   <  1:520191/69‑1 (MQ=255)
                        gTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACt                                >  1:2144267/1‑71 (MQ=255)
                        gTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACt                                >  1:532170/1‑71 (MQ=255)
                           aTCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTa                                                       <  1:547374/45‑1 (MQ=255)
                           aTCCGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAg                                         <  1:912424/59‑1 (MQ=255)
                             ccGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTa                                               >  1:2093618/1‑51 (MQ=255)
                             ccGTCTCGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGAGTAAAGTGTTACTGAAGGCGGCGACTGAGCa                           >  1:2414989/1‑71 (MQ=255)
                                tctcGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGaa                                          <  1:2352840/53‑1 (MQ=255)
                                  tcGGCGTGGCCTATGGCTCCGATCTGGAAAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCAc                          >  1:2583525/1‑68 (MQ=255)
                                  tcGGCGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCAccc                        >  1:800407/1‑69 (MQ=255)
                                    ggCGTGGCCTATGGCTCCGATCTGG‑AAAAGAGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCa                       <  1:1159268/68‑1 (MQ=255)
                                      cGTGGCCTATGGCTCCGATCTGG‑AAAAGTTCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGt                  <  1:773569/71‑1 (MQ=255)
                                      cGTGGCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGt                  <  1:1066026/71‑1 (MQ=255)
                                         ggCCTATGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGaa                                          <  1:1237162/44‑1 (MQ=39)
                                          gCCTATGGCTCCGATCTGGAAAAAGTGCGTAAAGTGTTACTGaa                                          >  1:720829/1‑44 (MQ=255)
                                               tGGCTCCGATCTGG‑AAAAGTGCGTAATGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGTGATGCAc           >  1:566265/1‑69 (MQ=255)
                                               tGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAg                     <  1:2159581/59‑1 (MQ=255)
                                               tGGCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAg                     <  1:279366/59‑1 (MQ=255)
                                                 gCTCCGATCTGG‑AAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGTGATGCACGAAc       >  1:942605/1‑71 (MQ=255)
                                                            gAAAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGTGATGCACGAACCAATg  <  1:1754738/66‑1 (MQ=255)
                                                             |                                                                
TTGACTGACACTACTACGCGTCTGGTGATCCGTCTCGGCGTGGCCTATGGCTCCGATCTGGAAAAAGTGCGTAAAGTGTTACTGAAGGCGGCGACTGAGCACCCAAGGGTGATGCACGAACCAATG  >  W3110S.gb/488745‑488870

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A