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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,996,085 C→T 37.2% A284V (GCC→GTC)  prlC → oligopeptidase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,996,0850CT37.2% 38.9 / 43.1 43A284V (GCC→GTC) prlColigopeptidase A
Reads supporting (aligned to +/- strand):  ref base C (12/15);  new base T (10/6);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 3.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.80e-01

CTCGCGCTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTGGCAAAACGCGCGCGTC  >  W3110S.gb/3996021‑3996153
                                                                |                                                                    
cTCGCGCTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTa                                                                 <  1:343898/70‑1 (MQ=255)
cTCGCGCTGCGTCACGAACTGGCACAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTaa                                                                <  1:2538112/71‑1 (MQ=255)
   gcgcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCa                                                                    >  1:3516528/1‑64 (MQ=255)
   gcgcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCa                                                                    >  1:3805799/1‑64 (MQ=255)
   gcgcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCa                                                                    >  1:194046/1‑64 (MQ=255)
   gcgcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTAAAAt                                                             >  1:1722595/1‑71 (MQ=255)
     gcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATgt                                                           >  1:2095955/1‑70 (MQ=255)
     gcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATgg                                                           >  1:3386481/1‑71 (MQ=255)
     gcTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATgg                                                           >  1:1793699/1‑71 (MQ=255)
          gTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGaa                                                      <  1:1208274/71‑1 (MQ=255)
           tCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGaa                                                      <  1:4296528/70‑1 (MQ=255)
                 aCTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCgc                                               <  1:2906022/71‑1 (MQ=255)
                 aCTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCgc                                               <  1:787715/71‑1 (MQ=255)
                     gcgcAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGAAAACCCgcag                                             <  1:3784839/69‑1 (MQ=255)
                     gcgcAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTaa                                                                <  1:564718/50‑1 (MQ=255)
                       gcAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGaa                                                      <  1:4325487/58‑1 (MQ=255)
                           ctgctgGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTaa                                                                <  1:3778264/44‑1 (MQ=255)
                           ctgctgGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTaa                                                                <  1:3680649/44‑1 (MQ=255)
                           ctgctgGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTaa                                                                <  1:531269/44‑1 (MQ=255)
                              ctgGGCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTgg                                   <  1:4343874/70‑1 (MQ=255)
                                  gCTTTGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTc                              >  1:4556571/1‑71 (MQ=255)
                                      tGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGAAAACCCgcagca                                           <  1:4159282/54‑1 (MQ=255)
                                      tGAAAACTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGAAAACCCgcag                                             >  1:822664/1‑52 (MQ=255)
                                      tGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCtt                            <  1:765820/69‑1 (MQ=255)
                                      tGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCtt                            <  1:469759/69‑1 (MQ=255)
                                       gAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGa                                                       <  1:2247686/41‑1 (MQ=255)
                                       gAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTACTTAAc                         >  1:4671333/1‑71 (MQ=255)
                                        aaaaCTACGCCTTTAAATCCCTTGTCACTAAAATGGCAGAAAACCCGCAGCAgg                                         >  1:367404/1‑54 (MQ=255)
                                          aaCTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGa                      <  1:2032599/71‑1 (MQ=255)
                                           aCTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGcagcag                                          >  1:2173443/1‑50 (MQ=255)
                                              aCGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTg                  >  1:1152842/1‑71 (MQ=255)
                                               cGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTgg                 >  1:414747/1‑71 (MQ=255)
                                                   tttAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCt                             <  1:2595103/55‑1 (MQ=255)
                                                   tttAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCt                             <  1:1748359/55‑1 (MQ=255)
                                                     tAAATCCCTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGAt                     >  1:3270374/1‑61 (MQ=255)
                                                     tAAATCCCTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATc                    >  1:3663202/1‑62 (MQ=255)
                                                     tAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTGGCaaaa            >  1:3368786/1‑70 (MQ=255)
                                                     tAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTGGCAAAAc           >  1:1825296/1‑71 (MQ=255)
                                                        aTCCCTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTa                           <  1:2366756/52‑1 (MQ=255)
                                                           ccTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTGGCAAAAcgcgcgc     >  1:1021944/1‑71 (MQ=255)
                                                            cTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGAttt                               >  1:1561407/1‑44 (MQ=255)
                                                            cTTGTCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGAttt                               >  1:1567181/1‑44 (MQ=255)
                                                               gCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTGGCAAAACGCGCGCGTc  >  1:1339541/1‑70 (MQ=255)
                                                                |                                                                    
CTCGCGCTGCGTCACGAACTGGCGCAACTGCTGGGCTTTGAAAACTACGCCTTTAAATCCCTTGCCACTAAAATGGCAGAAAACCCGCAGCAGGTGCTGGATTTCTTAACCGATCTGGCAAAACGCGCGCGTC  >  W3110S.gb/3996021‑3996153

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A