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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,863,059 G→A 11.5% L56L (CTG→CTA)  ygbM → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,863,0590GA11.5% 178.3 / 11.7 61L56L (CTG→CTA) ygbMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (29/25);  new base A (4/3);  total (33/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

AATTTCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCT  >  W3110S.gb/2862989‑2863118
                                                                      |                                                           
aaTTTCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTg                                                             >  1:504777/1‑71 (MQ=255)
    tCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGgcgc                                                         >  1:3215477/1‑71 (MQ=255)
        tttCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTg                                                       <  1:3955103/69‑1 (MQ=255)
          tCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTc                                                    <  1:4054656/70‑1 (MQ=255)
          tCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTc                                                    <  1:2169622/70‑1 (MQ=255)
            ccTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                  <  1:2510490/70‑1 (MQ=255)
            ccTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                  <  1:3965409/70‑1 (MQ=255)
            ccTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCaa                                                  <  1:3905617/70‑1 (MQ=255)
             cTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATa                                                <  1:4028167/71‑1 (MQ=255)
                taACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCt                                                        >  1:391971/1‑60 (MQ=255)
                      ctCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCg                                       <  1:3187711/71‑1 (MQ=255)
                      ctCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCg                                       <  1:3449549/71‑1 (MQ=255)
                      ctCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCg                                       <  1:3475488/71‑1 (MQ=255)
                       tCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAAt                                                 <  1:3875618/60‑1 (MQ=255)
                        ccACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCg                                       >  1:547256/1‑69 (MQ=255)
                         cACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGgc                                                           >  1:3175589/1‑48 (MQ=255)
                         cACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCg                                       >  1:661168/1‑68 (MQ=255)
                         cACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCg                                       >  1:2876889/1‑68 (MQ=255)
                           cccTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGat                                  <  1:2214689/71‑1 (MQ=255)
                           cccTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCa                                                   >  1:4179077/1‑54 (MQ=255)
                             cTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGatat                                >  1:504806/1‑71 (MQ=255)
                              tGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGatat                                >  1:56226/1‑70 (MQ=255)
                              tGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACAGCTCCCGGAGatat                                >  1:3396919/1‑70 (MQ=255)
                              tGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCaa                                                  <  1:2088820/52‑1 (MQ=255)
                               gCAAATCCAAAAGCAACTGTAGCAAAACCATCTGACACTGgc                                                           <  1:2548985/42‑1 (MQ=255)
                               gCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATa                                                >  1:190208/1‑53 (MQ=255)
                                cAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTaa                             >  1:1335363/1‑71 (MQ=255)
                                 aaaTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                  <  1:107024/49‑1 (MQ=255)
                                 aaaTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGgaga                                   >  1:2012831/1‑64 (MQ=255)
                                  aaTCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATAc                                               >  1:3879732/1‑51 (MQ=255)
                                   aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCg                                       >  1:2717397/1‑58 (MQ=255)
                                   aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                           >  1:4409846/1‑70 (MQ=255)
                                   aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGc                          >  1:1929314/1‑71 (MQ=255)
                                    tCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCg                         >  1:2098123/1‑71 (MQ=255)
                                     ccAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATAc                                               <  1:1215284/48‑1 (MQ=255)
                                     ccAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATAc                                               <  1:4314682/48‑1 (MQ=255)
                                     ccAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATAc                                               <  1:146114/48‑1 (MQ=255)
                                     ccAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATAtt                               <  1:9667/64‑1 (MQ=255)
                                     ccAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                           <  1:127533/68‑1 (MQ=255)
                                      cAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATTCCGCTCCCGGAGATATTAATGCgg                        <  1:800572/70‑1 (MQ=255)
                                       aaaaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGata                                 >  1:4616457/1‑60 (MQ=255)
                                        aaaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                  <  1:763844/42‑1 (MQ=255)
                                        aaaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGata                                 >  1:1577564/1‑59 (MQ=255)
                                         aaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATAc                                               >  1:4575496/1‑44 (MQ=255)
                                         aaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCggggg                     >  1:4067162/1‑70 (MQ=255)
                                         aaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCggg                       >  1:1292550/1‑68 (MQ=255)
                                         aaGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCgggg                      >  1:1522514/1‑69 (MQ=255)
                                             aaCTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATgg                >  1:3295709/1‑71 (MQ=255)
                                              aCTGGAGCAAATCCATCTGACACTGGCGCTGTTCaa                                                  <  1:2982588/36‑1 (MQ=255)
                                              aCTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                  <  1:2988082/36‑1 (MQ=255)
                                              aCTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATggg               <  1:265502/71‑1 (MQ=255)
                                               cTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATggg               >  1:1888387/1‑70 (MQ=255)
                                                 ggAGCAAAACCATCTGACACTGGCGCTGTTCAATa                                                >  1:2196779/1‑35 (MQ=255)
                                                 ggAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCgg                        >  1:3197733/1‑59 (MQ=255)
                                                  gAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                           >  1:2390600/1‑55 (MQ=255)
                                                  gAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                           >  1:2396044/1‑55 (MQ=255)
                                                   aGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGaa                   >  1:1208514/1‑62 (MQ=255)
                                                    gCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCg                         <  1:1388938/55‑1 (MQ=255)
                                                       aaaCCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCg      <  1:3599677/71‑1 (MQ=255)
                                                            aTCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCt  <  1:2942514/70‑1 (MQ=255)
                                                              cTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGc                          >  1:3591900/1‑44 (MQ=255)
                                                                     tGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGcc    >  1:103271/1‑59 (MQ=255)
                                                                      |                                                           
AATTTCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCT  >  W3110S.gb/2862989‑2863118

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A