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 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,350,232 G→A 11.9% R3C (CGC→TGC)  yjdF ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,350,2320GA11.9% 170.5 / 11.8 59R3C (CGC→TGC) yjdFconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (20/32);  new base A (3/4);  total (23/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.34e-01

ATGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGC  >  W3110S.gb/4350162‑4350300
                                                                      |                                                                    
aTGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCg                                                                      >  1:4430316/1‑71 (MQ=255)
       tataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                               <  1:446162/71‑1 (MQ=255)
       tataAATCAGGATTAACGTTAGCGTCACTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                               <  1:145933/71‑1 (MQ=255)
        ataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATgg                                                              >  1:1208051/1‑71 (MQ=255)
         taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATgg                                                              <  1:4197226/70‑1 (MQ=255)
         taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                             >  1:4142756/1‑71 (MQ=255)
           aaTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                             >  1:3913141/1‑69 (MQ=255)
           aaTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTg                                                            <  1:1257750/70‑1 (MQ=255)
            aTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAg                                                          <  1:2818982/71‑1 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                         <  1:727107/71‑1 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                         <  1:2305619/71‑1 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                         <  1:809534/71‑1 (MQ=255)
              cAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGa                                                           >  1:924712/1‑68 (MQ=255)
               aGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCggg                                                                    <  1:90299/58‑1 (MQ=255)
               aGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCggg                                                                    <  1:1187332/58‑1 (MQ=255)
               aGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTc                                                       <  1:549298/71‑1 (MQ=255)
                 gATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGc                                                     <  1:1691845/71‑1 (MQ=255)
                 gATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTc                                                                  <  1:965840/58‑1 (MQ=255)
                   ttAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                    >  1:3858534/1‑70 (MQ=255)
                   ttAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                    >  1:3985726/1‑70 (MQ=255)
                    tAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCaaa                                                  >  1:285278/1‑71 (MQ=255)
                     aaCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCaaa                                                  <  1:343217/70‑1 (MQ=255)
                     aaCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCaaa                                                  <  1:2894512/70‑1 (MQ=255)
                     aaCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAAt                                                 >  1:2255168/1‑71 (MQ=255)
                      aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAAt                                                 <  1:4331429/70‑1 (MQ=255)
                        gTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTc                                                       >  1:1888073/1‑62 (MQ=255)
                        gTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAg                                              <  1:1695416/71‑1 (MQ=255)
                         ttAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAgg                                             <  1:898102/71‑1 (MQ=255)
                         ttAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCa                                                                 <  1:893087/51‑1 (MQ=255)
                           aGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                             >  1:4120796/1‑53 (MQ=255)
                           aGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAggg                                            >  1:841285/1‑70 (MQ=255)
                            gCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                               <  1:2585529/50‑1 (MQ=255)
                              gTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaaaa                                        <  1:2327542/71‑1 (MQ=255)
                               tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                             <  1:4573753/49‑1 (MQ=255)
                               tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaaaa                                        <  1:2350547/70‑1 (MQ=255)
                                 aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATAc                                     >  1:2347377/1‑71 (MQ=255)
                                 aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATAc                                     >  1:4514703/1‑71 (MQ=255)
                                   tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGa                                                           >  1:1620876/1‑47 (MQ=255)
                                   tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCATGGAAAATACTg                                   <  1:4461841/71‑1 (MQ=255)
                                   tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTg                                   <  1:1175327/71‑1 (MQ=255)
                                    gcgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGa                                  >  1:2592640/1‑71 (MQ=255)
                                       cTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTa                               <  1:4207729/71‑1 (MQ=255)
                                          gtgtTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTAtt                             <  1:1939500/70‑1 (MQ=255)
                                             ttAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCAc                          <  1:537778/70‑1 (MQ=255)
                                               aaGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATa                                      >  1:2705637/1‑56 (MQ=255)
                                               aaGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATa                                      >  1:2711210/1‑56 (MQ=255)
                                                aGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGc                      <  1:2145782/71‑1 (MQ=255)
                                                 gAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGc                      >  1:2807832/1‑70 (MQ=255)
                                                     tAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAggg                                            <  1:3721307/44‑1 (MQ=255)
                                                       aCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAAt                                       <  1:1664673/47‑1 (MQ=255)
                                                        cGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTc                            <  1:2311325/57‑1 (MQ=255)
                                                        cGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTg               >  1:3001012/1‑70 (MQ=255)
                                                         ggCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCAc                          <  1:120879/58‑1 (MQ=255)
                                                         ggCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGa              <  1:725089/70‑1 (MQ=255)
                                                              gAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTa         >  1:2716891/1‑70 (MQ=255)
                                                               aGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTAc        <  1:3701997/70‑1 (MQ=255)
                                                               aGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTAc        <  1:37002/70‑1 (MQ=255)
                                                                gtgtGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACaa      >  1:410613/1‑71 (MQ=255)
                                                                 tgtgCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaaa            <  1:2693502/64‑1 (MQ=255)
                                                                   tgCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCg   <  1:1915448/71‑1 (MQ=255)
                                                                     cGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGa              >  1:3831990/1‑58 (MQ=255)
                                                                     cGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGc  >  1:476549/1‑70 (MQ=255)
                                                                      |                                                                    
ATGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGC  >  W3110S.gb/4350162‑4350300

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