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 3,306,434 G→A 33.3% L428L (CTG→TTG)  deaD ← ATP‑dependent RNA helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,306,4340GA33.3% 73.9 / 53.9 60L428L (CTG→TTG) deaDATP‑dependent RNA helicase
Reads supporting (aligned to +/- strand):  ref base G (25/15);  new base A (6/14);  total (31/29)
Fisher's exact test for biased strand distribution p-value = 2.78e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.49e-01

CGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTCAG  >  W3110S.gb/3306376‑3306497
                                                          |                                                               
cGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCag                                                     <  1:4970383/71‑1 (MQ=255)
  cATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCagag                                                   >  1:1063968/1‑71 (MQ=255)
    tCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGtt                                                 <  1:2802052/71‑1 (MQ=255)
    tCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGtt                                                 <  1:1149536/71‑1 (MQ=255)
    tCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGtt                                                 <  1:1997272/71‑1 (MQ=255)
    tCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGtt                                                 >  1:400794/1‑71 (MQ=255)
      ggCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                               >  1:4018349/1‑71 (MQ=255)
       gcgcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCg                                              <  1:1375778/71‑1 (MQ=255)
         gcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                               >  1:1708629/1‑68 (MQ=255)
         gcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCgag                                            <  1:3149509/71‑1 (MQ=255)
         gcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCgag                                            <  1:2240027/71‑1 (MQ=255)
          cATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCgag                                            <  1:3406650/70‑1 (MQ=255)
             cTGGCGATACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATc                                         >  1:654989/1‑70 (MQ=255)
              tGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATc                                         >  1:1390785/1‑69 (MQ=255)
              tGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATc                                         >  1:1107762/1‑69 (MQ=255)
               ggCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGt                                                  <  1:3106783/59‑1 (MQ=255)
                gCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTTCCGCAGCCAGAGTTTCGAGATcc                                        <  1:345999/68‑1 (MQ=255)
                gCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATcc                                        <  1:618142/68‑1 (MQ=255)
                 cGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGct                                    <  1:497519/71‑1 (MQ=255)
                  ggTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCagag                                                   >  1:2394386/1‑55 (MQ=255)
                   gTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCaga                                                    <  1:3312310/53‑1 (MQ=255)
                     aCGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGttt                                                >  1:5001575/1‑55 (MQ=255)
                     aCGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGc                                     >  1:4016753/1‑66 (MQ=255)
                     aCGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCtt                                 >  1:3854104/1‑70 (MQ=255)
                      cGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCa                               <  1:4715112/71‑1 (MQ=255)
                      cGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTc                                <  1:2166239/70‑1 (MQ=255)
                        aTCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCag                                                     <  1:804022/47‑1 (MQ=255)
                        aTCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                               >  1:1276662/1‑53 (MQ=255)
                        aTCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                               >  1:3522010/1‑53 (MQ=255)
                        aTCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                               >  1:2499522/1‑53 (MQ=255)
                        aTCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGctc                                   <  1:2918480/65‑1 (MQ=255)
                           agagTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCga                                             >  1:2948862/1‑52 (MQ=255)
                           agagTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCga                                             >  1:2999975/1‑52 (MQ=255)
                           agagTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCga                                             >  1:132769/1‑52 (MQ=255)
                           agagTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTc                          <  1:3945434/71‑1 (MQ=255)
                            gagTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                               <  1:29285/49‑1 (MQ=255)
                             agTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTcag                        <  1:3336382/71‑1 (MQ=255)
                             agTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTcag                        <  1:2421997/71‑1 (MQ=255)
                                 cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGtt                                                 >  1:4388209/1‑42 (MQ=255)
                                 cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGt                    >  1:2033128/1‑71 (MQ=255)
                                 cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGt                    >  1:2977118/1‑71 (MQ=255)
                                 cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGt                    >  1:1089109/1‑71 (MQ=255)
                                 cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGt                    >  1:3904240/1‑71 (MQ=255)
                                   ttCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCAc                              >  1:3266925/1‑59 (MQ=255)
                                   ttCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCAc                              >  1:1680601/1‑59 (MQ=255)
                                         cTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGc                                     <  1:3742742/46‑1 (MQ=255)
                                          tgtgCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATcc                                        >  1:1049658/1‑42 (MQ=255)
                                          tgtgCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGct                                    >  1:4309721/1‑46 (MQ=255)
                                           gtgCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAtt          >  1:3745464/1‑71 (MQ=255)
                                            tgCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAt           <  1:1600240/69‑1 (MQ=255)
                                            tgCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAt           <  1:2782888/69‑1 (MQ=255)
                                            tgCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAt           <  1:2858022/69‑1 (MQ=255)
                                                 ttttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGc                                     <  1:4927286/38‑1 (MQ=255)
                                                 ttttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCt     >  1:2815401/1‑70 (MQ=255)
                                                  tttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTc    >  1:3361277/1‑70 (MQ=255)
                                                   ttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTcag  >  1:4612341/1‑71 (MQ=255)
                                                   ttCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTcag  >  1:1644477/1‑71 (MQ=255)
                                                    tCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTcag  <  1:4608708/70‑1 (MQ=255)
                                                    tCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTcag  <  1:1730300/70‑1 (MQ=255)
                                                    tCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTcag  <  1:408411/70‑1 (MQ=255)
                                                       gcaaTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTg              <  1:1966595/55‑1 (MQ=255)
                                                          |                                                               
CGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTCAG  >  W3110S.gb/3306376‑3306497

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