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 3,712,033 G→A 25.4% M328I (ATG→ATA)  gidA → glucose‑inhibited cell‑division protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,712,0330GA25.4% 97.3 / 33.6 55M328I (ATG→ATA) gidAglucose‑inhibited cell‑division protein
Reads supporting (aligned to +/- strand):  ref base G (25/16);  new base A (9/5);  total (34/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.40e-01

TTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATCCT  >  W3110S.gb/3711969‑3712099
                                                                |                                                                  
tttATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAggg                                                               >  1:1839438/1‑70 (MQ=255)
      cGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGaa                                                        <  1:3152231/71‑1 (MQ=255)
                 tcCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGaaa                                                       >  1:1855730/1‑61 (MQ=255)
                   caccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAg                                               <  1:321355/67‑1 (MQ=255)
                   caccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATc                                            <  1:3892395/70‑1 (MQ=255)
                     ccaGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTg                                         >  1:3263205/1‑71 (MQ=255)
                         ccTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGAt                                             <  1:3067756/63‑1 (MQ=255)
                           tGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCg                                           >  1:766080/1‑63 (MQ=255)
                            gCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCgg                                  >  1:2749309/1‑71 (MQ=255)
                             ccGTTCGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCggg                                 >  1:3234494/1‑71 (MQ=255)
                              cGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                <  1:4345367/71‑1 (MQ=255)
                              cGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                <  1:944343/71‑1 (MQ=255)
                              cGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCCTCCGGGt                                <  1:3639237/71‑1 (MQ=255)
                               gTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                <  1:252274/70‑1 (MQ=255)
                                ttCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGAt                                             <  1:251853/56‑1 (MQ=255)
                                 tCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTAt                             >  1:2994045/1‑71 (MQ=255)
                                  cGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTAt                             >  1:2382374/1‑70 (MQ=255)
                                  cGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATg                            >  1:3762103/1‑71 (MQ=255)
                                  cGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATg                            >  1:1967957/1‑71 (MQ=255)
                                  cGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATg                            >  1:1836558/1‑71 (MQ=255)
                                  cGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGaaa                                                       >  1:4411781/1‑44 (MQ=255)
                                  cGATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTAt                             >  1:3418452/1‑70 (MQ=255)
                                   gATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGc                           <  1:3818358/71‑1 (MQ=255)
                                   gATGTGCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGc                           <  1:1723193/71‑1 (MQ=255)
                                     tgtgCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCa                         >  1:1322646/1‑71 (MQ=255)
                                      gtgCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGt                                >  1:854745/1‑63 (MQ=255)
                                       tgCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAg                                               <  1:1939775/47‑1 (MQ=255)
                                       tgCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAg                                               <  1:888135/47‑1 (MQ=255)
                                        gCAGATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCAtt                       >  1:2526546/1‑70 (MQ=255)
                                         cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGaa                                                        >  1:2119089/1‑36 (MQ=255)
                                         cAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTg                      <  1:4155191/70‑1 (MQ=255)
                                           gATGCAAATCGTCCGCTCTATACAGGGGATGGAAAAcgcg                                                  <  1:3264128/40‑1 (MQ=255)
                                           gATGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCAtt                       >  1:135375/1‑67 (MQ=255)
                                             tGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGtt                               <  1:993885/57‑1 (MQ=255)
                                             tGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGtt                               <  1:3050902/57‑1 (MQ=255)
                                             tGCAAATCGTCCGCTCTATACAGGGGATGGAAAACGCGaa                                                >  1:4166329/1‑40 (MQ=255)
                                              gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTa                              >  1:10809/1‑57 (MQ=255)
                                              gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTa                              >  1:2232132/1‑57 (MQ=255)
                                              gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTa                              >  1:1352121/1‑57 (MQ=255)
                                              gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTa                              >  1:4367743/1‑57 (MQ=255)
                                              gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 >  1:132193/1‑70 (MQ=255)
                                              gCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTAt                 >  1:40783/1‑70 (MQ=255)
                                                 aaTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATc                                            >  1:1183828/1‑40 (MQ=255)
                                                 aaTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATc                                            >  1:4008406/1‑40 (MQ=255)
                                                  aTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGActt            >  1:3370594/1‑71 (MQ=255)
                                                  aTCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGAct             >  1:539140/1‑70 (MQ=255)
                                                     gTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTc                                     >  1:3286048/1‑43 (MQ=255)
                                                     gTCCGCTCTATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGActtctt         <  1:2112133/71‑1 (MQ=255)
                                                        cGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCg       <  1:1503641/70‑1 (MQ=255)
                                                        cGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGa      <  1:4278741/71‑1 (MQ=255)
                                                        cGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGa      >  1:3039460/1‑71 (MQ=255)
                                                            ctATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATCCt  >  1:2486137/1‑71 (MQ=255)
                                                            ctATACAGGGGATGGAAAACGCGAAGATCGTGCGTc                                     >  1:3836552/1‑36 (MQ=255)
                                                            ctATACAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGa               >  1:1782797/1‑58 (MQ=255)
                                                             tATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATcc   <  1:56581/69‑1 (MQ=255)
                                                                |                                                                  
TTTATCCGAACGGTATCTCCACCAGCCTGCCGTTCGATGTGCAGATGCAAATCGTCCGCTCTATGCAGGGGATGGAAAACGCGAAGATCGTGCGTCCGGGTTATGCCATTGAGTATGACTTCTTCGATCCT  >  W3110S.gb/3711969‑3712099

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