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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,538,437 G→A 16.9% A170V (GCA→GTA)  rhaS ← DNA‑binding transcriptional activator, L‑rhamnose‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,538,4370GA16.9% 143.9 / 20.5 59A170V (GCA→GTA) rhaSDNA‑binding transcriptional activator, L‑rhamnose‑binding
Reads supporting (aligned to +/- strand):  ref base G (26/23);  new base A (8/2);  total (34/25)
Fisher's exact test for biased strand distribution p-value = 1.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

GCATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGATC  >  W3110S.gb/3538371‑3538505
                                                                  |                                                                    
gCATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCt                                                                  <  1:3201094/71‑1 (MQ=255)
 cATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTg                                                                 <  1:44603/71‑1 (MQ=255)
 cATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTg                                                                 <  1:1450558/71‑1 (MQ=255)
   tCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGtt                                                               <  1:3211784/71‑1 (MQ=255)
       aaTTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTcc                                                           <  1:981194/71‑1 (MQ=255)
       aaTTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTcc                                                           <  1:810372/71‑1 (MQ=255)
        aTTCACCTCATCGGCAAAATGGTCGTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGtttt                                                             >  1:2535232/1‑68 (MQ=255)
         ttCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAg                                                         >  1:3206824/1‑71 (MQ=255)
              cTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTtct                                                    >  1:3565639/1‑71 (MQ=255)
               tCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCt                                                                  <  1:2420112/56‑1 (MQ=255)
                cATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTcc                                                  >  1:1484453/1‑71 (MQ=255)
                cATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTcc                                                  >  1:4536053/1‑71 (MQ=255)
                    ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGc                                               >  1:4485175/1‑70 (MQ=255)
                    ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGc                                               >  1:4206095/1‑70 (MQ=255)
                    ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCt                                                 >  1:1120675/1‑68 (MQ=255)
                    ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAACTTGAGACGTGATGCGCTGt                                                                <  1:615585/53‑1 (MQ=255)
                     gCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCa                                              <  1:2814191/70‑1 (MQ=255)
                      cAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGttt                                                              >  1:1109377/1‑53 (MQ=255)
                        aaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAg                                                         >  1:924/1‑56 (MQ=255)
                        aaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACt                                          <  1:3648851/71‑1 (MQ=255)
                        aaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACt                                          >  1:4055402/1‑71 (MQ=255)
                         aaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAAATg                                         >  1:580913/1‑71 (MQ=255)
                           tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTtct                                                    <  1:4045020/58‑1 (MQ=255)
                           tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGtt                                                               >  1:659306/1‑47 (MQ=255)
                           tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGtt                                                               >  1:2847610/1‑47 (MQ=255)
                            ggTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTcc                                                           >  1:1808997/1‑50 (MQ=255)
                             gTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCa                                                          >  1:2485765/1‑50 (MQ=255)
                             gTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCttt                                     <  1:2872985/71‑1 (MQ=255)
                              tcctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCtttt                                    <  1:428897/71‑1 (MQ=255)
                                ctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTg                                                                 <  1:1568350/40‑1 (MQ=255)
                                ctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTg                                         <  1:68759/64‑1 (MQ=255)
                                 tccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCa                                              <  1:3645738/58‑1 (MQ=255)
                                  ccagccagGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTa                                   >  1:1623616/1‑68 (MQ=255)
                                  ccagccagGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACg                                 >  1:2277075/1‑70 (MQ=255)
                                  ccagccagGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCt                                       >  1:2686230/1‑64 (MQ=255)
                                   cagccagGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCaaa                                            >  1:4031323/1‑58 (MQ=255)
                                              gAAGCAAGTTGAGACGTGATGCGCTGTTTT‑CAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTa                   <  1:2131123/71‑1 (MQ=255)
                                              gAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAagag                        >  1:1015349/1‑67 (MQ=255)
                                               aaGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGc                                        <  1:2736049/50‑1 (MQ=255)
                                               aaGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt                    >  1:2084628/1‑70 (MQ=255)
                                                aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTtctc                                                   >  1:2594608/1‑38 (MQ=255)
                                                aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAaga                         >  1:1130789/1‑64 (MQ=255)
                                                aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa                  >  1:2013397/1‑71 (MQ=255)
                                                aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTa                   <  1:663020/70‑1 (MQ=255)
                                                 gCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAAt                 >  1:2911338/1‑71 (MQ=255)
                                                   aaGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCa                                              <  1:1291831/40‑1 (MQ=255)
                                                     gTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCtttt                                    <  1:4255757/48‑1 (MQ=255)
                                                     gTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCtttt                                    <  1:2977815/48‑1 (MQ=255)
                                                      ttGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCa             >  1:209872/1‑70 (MQ=255)
                                                        gagaCGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCaa                           >  1:1242068/1‑54 (MQ=255)
                                                        gagaCGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa                  >  1:3912396/1‑63 (MQ=255)
                                                             gTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAg     <  1:1651071/71‑1 (MQ=255)
                                                              tGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCa                      >  1:429108/1‑53 (MQ=255)
                                                              tGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCa                      >  1:2466585/1‑53 (MQ=255)
                                                              tGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAg     <  1:3939980/70‑1 (MQ=255)
                                                                aTGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCtttt                                    >  1:1784638/1‑37 (MQ=255)
                                                                aTGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGAtc  >  1:535889/1‑71 (MQ=255)
                                                                aTGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGAtc  <  1:3461196/71‑1 (MQ=255)
                                                                 tGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCa                      >  1:4542387/1‑50 (MQ=255)
                                                                  gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt                    <  1:1223242/51‑1 (MQ=255)
                                                                  gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt                    <  1:3031990/51‑1 (MQ=255)
                                                                  |                                                                    
GCATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGATC  >  W3110S.gb/3538371‑3538505

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