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 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 478,343 C→T 8.3% A45T (GCT→ACT)  ylaC ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb478,3430CT 8.3% 187.7 / 6.1 60A45T (GCT→ACT) ylaCpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (34/21);  new base T (2/3);  total (36/24)
Fisher's exact test for biased strand distribution p-value = 3.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

CAACCAGTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCGGGGTTTGTTGTC  >  W3110S.gb/478274‑478412
                                                                     |                                                                     
cAACCAGTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCa                                                                      <  1:1346048/71‑1 (MQ=255)
cAACCAGTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCa                                                                      <  1:2703620/71‑1 (MQ=255)
   ccAGTAGCCAGACAGAGCCTGACAGCGTTTCGGAGTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACg                                                                   <  1:3196038/71‑1 (MQ=255)
    cAGTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACg                                                                   >  1:217229/1‑70 (MQ=255)
     aGTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTa                                                                 <  1:2987740/71‑1 (MQ=255)
      gTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTa                                                                 >  1:2736271/1‑70 (MQ=255)
         gCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGTAACGTACAt                                                              <  1:1247481/70‑1 (MQ=255)
         gCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACAt                                                              <  1:4103873/70‑1 (MQ=255)
         gCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATa                                                             >  1:3319629/1‑71 (MQ=255)
         gCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATa                                                             >  1:3622494/1‑71 (MQ=255)
            agacagaGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATAcc                                                           >  1:1488887/1‑70 (MQ=255)
              acagaGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACa                                                               <  1:206402/64‑1 (MQ=255)
              acagaGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGAt                                                        <  1:1843037/71‑1 (MQ=255)
                agagCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGTCAAAAAAAGCAACGTACa                                                               >  1:2494128/1‑62 (MQ=255)
                agagCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATAcc                                                           <  1:934022/66‑1 (MQ=255)
                    ccTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGTAACGTACATACCGATAAACAg                                                  <  1:323340/71‑1 (MQ=255)
                     cTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGc                                                 <  1:961990/71‑1 (MQ=255)
                      tGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGc                                                                       <  1:1587988/48‑1 (MQ=255)
                      tGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGc                                                                       <  1:3836263/48‑1 (MQ=255)
                         cAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCg                                             >  1:1991244/1‑71 (MQ=255)
                         cAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCg                                             <  1:2652/71‑1 (MQ=255)
                         cAGCGTTTCGGACTGCAAAATCACCGCCTGGGTGGCAAAAAAAGCAACGTACATACCGATAAACTGCCCCg                                             <  1:555620/71‑1 (MQ=255)
                          aGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCg                                             >  1:931900/1‑70 (MQ=255)
                           gCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGa                                           >  1:617688/1‑71 (MQ=255)
                            cGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGa                                           >  1:2859978/1‑70 (MQ=255)
                             gTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATg                                         >  1:3756053/1‑71 (MQ=255)
                               ttCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGtt                                       >  1:2880017/1‑71 (MQ=255)
                                tCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACa                                                               >  1:4163599/1‑46 (MQ=255)
                                tCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGcc                                                >  1:3128933/1‑61 (MQ=255)
                                tCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGtt                                       <  1:4217610/70‑1 (MQ=255)
                                 cGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTa                                     >  1:1498332/1‑71 (MQ=255)
                                  ggACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTAc                                    <  1:691353/71‑1 (MQ=255)
                                   gACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTAc                                                                >  1:813604/1‑42 (MQ=255)
                                     cTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGa                                 >  1:2993474/1‑71 (MQ=255)
                                      tGCAACATCACCGCCAGGGTTGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGa                                 >  1:681754/1‑70 (MQ=255)
                                        cAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATa                               >  1:2651141/1‑70 (MQ=255)
                                         aaCATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACATCCGGGGCTGTTTatc                                   >  1:3435621/1‑63 (MQ=37)
                                         aaCATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATaa                              >  1:2227296/1‑70 (MQ=255)
                                          aCATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATaaa                                                     >  1:3327130/1‑46 (MQ=255)
                                          aCATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATaaaa                            <  1:464730/71‑1 (MQ=255)
                                           cATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAAc                           >  1:3543271/1‑71 (MQ=255)
                                            aTCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTa                                     >  1:1151704/1‑60 (MQ=255)
                                              cACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATaaa                                                     >  1:3680553/1‑42 (MQ=255)
                                              cACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGa                        >  1:1988976/1‑71 (MQ=255)
                                                  gCCAGGGTGGCAAAAAAAGTAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATAc                     >  1:2713918/1‑70 (MQ=255)
                                                    cAGGGTGGCAAAAAAAGTAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTa                   >  1:840914/1‑70 (MQ=255)
                                                     aGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGt                                        >  1:1727033/1‑48 (MQ=255)
                                                          cgCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGTATaaaa                            <  1:4058001/54‑1 (MQ=255)
                                                           gCAAAAAAAGTAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCgg             <  1:753756/69‑1 (MQ=255)
                                                            cAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATaa                              <  1:1865755/51‑1 (MQ=255)
                                                             aaaaaaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAg                >  1:2938505/1‑64 (MQ=255)
                                                              aaaaaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCGGGGtt         <  1:1731209/70‑1 (MQ=255)
                                                               aaaaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTa                                     >  1:2381990/1‑41 (MQ=255)
                                                               aaaaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATaaaa                            >  1:3811102/1‑50 (MQ=255)
                                                               aaaaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCGGGGTttg       >  1:1835901/1‑71 (MQ=255)
                                                                aaaaGCAACGTACATACCGATAAACAGCCCCGGATGtt                                       >  1:2452989/1‑38 (MQ=255)
                                                                aaaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATa                               <  1:255442/46‑1 (MQ=255)
                                                                 aaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACg                                   >  1:670705/1‑41 (MQ=255)
                                                                 aaaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACg                                   >  1:1439207/1‑41 (MQ=255)
                                                                  aaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAg                <  1:2389742/59‑1 (MQ=255)
                                                                  aaGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCGGGGTttgttg    <  1:2946884/71‑1 (MQ=255)
                                                                    gCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCGGGGTTTGTTGTc  <  1:4045325/71‑1 (MQ=255)
                                                                     |                                                                     
CAACCAGTAGCCAGACAGAGCCTGACAGCGTTTCGGACTGCAACATCACCGCCAGGGTGGCAAAAAAAGCAACGTACATACCGATAAACAGCCCCGGATGTTTACGGATAAAACTGATACTAAAGCGGGGTTTGTTGTC  >  W3110S.gb/478274‑478412

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