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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,698,594 A→G 26.0% L58S (TTG→TCG)  uidR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,698,5940AG26.0% 81.0 / 32.9 50L58S (TTG→TCG) uidRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (18/19);  new base G (5/8);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 7.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.04e-01

ATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATGGCTTT  >  W3110S.gb/1698534‑1698664
                                                            |                                                                      
aTCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCttt                                                              >  1:2995329/1‑71 (MQ=255)
        ccGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGa                                                      <  1:2195007/71‑1 (MQ=255)
         cGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGaa                                                     <  1:3382209/71‑1 (MQ=255)
         cGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGaa                                                     <  1:190840/71‑1 (MQ=255)
           gAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGgaga                                                         >  1:2227698/1‑65 (MQ=255)
              aCGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGt                                                <  1:3212379/71‑1 (MQ=255)
                gggCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAATGGTGa                                              <  1:3166464/71‑1 (MQ=255)
                gggCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                              <  1:3457100/71‑1 (MQ=255)
                       cgcCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGa                                                      <  1:2954316/56‑1 (MQ=255)
                       cgcCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGa                                                      <  1:708921/56‑1 (MQ=255)
                           ctctCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGaaa                                                    >  1:3742840/1‑54 (MQ=255)
                            tctcCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATg                                                  <  1:805290/55‑1 (MQ=255)
                            tctcCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATg                                                  <  1:3627613/55‑1 (MQ=255)
                             ctcCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                              >  1:3263948/1‑58 (MQ=255)
                               ccTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTccc                                   >  1:3030717/1‑67 (MQ=255)
                                cTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCgg                                 <  1:739813/68‑1 (MQ=255)
                                   gTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTaa                           >  1:2989381/1‑71 (MQ=255)
                                   gTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTaa                           >  1:2792140/1‑71 (MQ=255)
                                      cTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGaaa                                                    >  1:1436583/1‑43 (MQ=255)
                                      cTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATaga                                          <  1:1018248/53‑1 (MQ=255)
                                      cTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATaga                                          <  1:288349/53‑1 (MQ=255)
                                       tGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                             <  1:1372221/65‑1 (MQ=255)
                                       tGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCgg                                 <  1:2878076/61‑1 (MQ=255)
                                        gTAAGATAATCGCCTGAATCAAGGCTTCTTTGgag                                                          >  1:858064/1‑35 (MQ=255)
                                         tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTc                                     >  1:3636519/1‑55 (MQ=255)
                                         tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTc                                     >  1:2480655/1‑55 (MQ=255)
                                         tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                             <  1:2539148/63‑1 (MQ=255)
                                         tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                             <  1:3579611/63‑1 (MQ=255)
                                         tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGgcg                      >  1:1643623/1‑70 (MQ=255)
                                         tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGgcg                      >  1:825723/1‑70 (MQ=255)
                                              tAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAt                >  1:292761/1‑71 (MQ=255)
                                              tAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAt                >  1:1858944/1‑71 (MQ=255)
                                              tAATCGCCTGAAT‑AAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAtt               >  1:2152084/1‑71 (MQ=255)
                                               aaTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAtt               >  1:1189608/1‑71 (MQ=255)
                                               aaTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAtt               >  1:3237820/1‑71 (MQ=255)
                                               aaTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAtt               >  1:2365647/1‑71 (MQ=255)
                                                aTCGCCTGAATCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGAtt               >  1:80908/1‑70 (MQ=255)
                                                aTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                              >  1:994014/1‑39 (MQ=255)
                                                aTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                              >  1:2270754/1‑39 (MQ=255)
                                                   gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGTCTAATGGCGCAAGATTTACa           <  1:3186024/71‑1 (MQ=255)
                                                   gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTaa                           >  1:1460573/1‑55 (MQ=255)
                                                   gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:2661101/71‑1 (MQ=255)
                                                   gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:438273/71‑1 (MQ=255)
                                                   gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:3243588/71‑1 (MQ=255)
                                                   gCCTGAATCAAGGCTTCTTTAGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:985686/71‑1 (MQ=255)
                                                    ccTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                             <  1:3731892/52‑1 (MQ=255)
                                                    ccTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:550753/70‑1 (MQ=255)
                                                          tCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:2719424/64‑1 (MQ=255)
                                                          tCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:1913409/64‑1 (MQ=255)
                                                          tCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa           <  1:891026/64‑1 (MQ=255)
                                                            aaGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATGGCttt  >  1:4009139/1‑71 (MQ=255)
                                                            aaGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATGGCttt  >  1:428618/1‑71 (MQ=255)
                                                            aaGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATGGCttt  >  1:1626743/1‑71 (MQ=255)
                                                            |                                                                      
ATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATGGCTTT  >  W3110S.gb/1698534‑1698664

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