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
A6 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,813,392 G→A 49.1% R595R (CGC→CGT)  alaS ← alanyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,813,3920GA49.1% ‑0.6 / 79.1 55R595R (CGC→CGT) alaSalanyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base G (10/18);  new base A (14/13);  total (24/31)
Fisher's exact test for biased strand distribution p-value = 2.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

TGTGTTCACCAGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTGGCGCAGCGCAG  >  minE/1813323‑1813462
                                                                     |                                                                      
tgtgtTCACCAGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAg                                                                        <  1:1632321/70‑1 (MQ=255)
  tgtTCACCAGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAacg                                                                      <  1:1120198/70‑1 (MQ=255)
      cACCAGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGGCGAAGCgcagc                                                                  <  1:1595266/70‑1 (MQ=255)
         cAGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCt                                                              <  1:2705023/71‑1 (MQ=255)
          aGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCtt                                                             >  1:1846031/1‑71 (MQ=255)
               ttCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAgc                                                                       <  1:2079970/56‑1 (MQ=255)
               ttCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCgcagc                                                                  <  1:676696/61‑1 (MQ=255)
               ttCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCgcagc                                                                  <  1:2900183/61‑1 (MQ=255)
                 cGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAacg                                                                      >  1:990376/1‑55 (MQ=255)
                 cGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCAc                                                                >  1:2368769/1‑61 (MQ=255)
                 cGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGtt                                                       <  1:1227694/70‑1 (MQ=255)
                  gACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGtt                                                       >  1:3530416/1‑69 (MQ=255)
                  gACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTaa                                                     >  1:3175055/1‑71 (MQ=255)
                       cACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGt                                                <  1:242322/71‑1 (MQ=255)
                        aCGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTg                                               <  1:569657/71‑1 (MQ=255)
                        aCGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGt                                                >  1:2047936/1‑70 (MQ=255)
                         cGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCAc                                                                >  1:180492/1‑53 (MQ=255)
                          gAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGaa                                             <  1:2435717/71‑1 (MQ=255)
                           aaTCTCTTCTGGTTTCATCGCTTCGTTTTGTGAGAAGTCGAAGCGCAGCACCTTGt                                                           <  1:2496358/56‑1 (MQ=255)
                            aTCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAAcc                                           >  1:518425/1‑71 (MQ=255)
                                cttctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTc                                       >  1:1261305/1‑71 (MQ=255)
                                cttctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACAAGTGAACCTTTc                                       >  1:2721782/1‑71 (MQ=255)
                                 ttctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCtt                                         <  1:273510/68‑1 (MQ=255)
                                 ttctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCt                                          <  1:1677040/67‑1 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCAcc                                                               >  1:570203/1‑44 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGaa                                             >  1:2692333/1‑62 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGaa                                             >  1:1068585/1‑62 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTc                                       <  1:2543399/68‑1 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTc                                       <  1:3690409/68‑1 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAATCAGTGAACCTTTc                                       <  1:1162497/68‑1 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTc                                       <  1:2638725/68‑1 (MQ=255)
                                   ctGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTc                                       <  1:353292/68‑1 (MQ=255)
                                    tGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCttt                                        >  1:3680992/1‑66 (MQ=255)
                                    tGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCttt                                        >  1:3564860/1‑66 (MQ=255)
                                      gTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGa                                  <  1:1019648/70‑1 (MQ=255)
                                      gTTTCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGa                                  >  1:3706308/1‑70 (MQ=255)
                                       tttCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCt                                                              <  1:466702/41‑1 (MQ=255)
                                         tCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACa                              >  1:3207534/1‑71 (MQ=255)
                                         tCATCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACa                              >  1:3721674/1‑71 (MQ=255)
                                            tCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGa                           <  1:3262466/71‑1 (MQ=255)
                                            tCGCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGa                           <  1:199931/71‑1 (MQ=255)
                                              gCTTCGTTGTGTGAGAAGTCGAAACGCAGCACCTTGTCGTTAACAAGTGAACCTTTCTGCGATACATGAg                          >  1:673669/1‑70 (MQ=255)
                                                ttCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTAc                       >  1:499947/1‑71 (MQ=255)
                                                  cGTTGTGTGAGAAGTCTAAGCGCAGCACCTTGTCGTTAACCa                                                  <  1:1362723/42‑1 (MQ=255)
                                                  cGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCa                                                  <  1:3260063/42‑1 (MQ=255)
                                                   gTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGa                                  <  1:1675756/57‑1 (MQ=255)
                                                    ttGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCt                                          <  1:1691861/48‑1 (MQ=255)
                                                    ttGTGGGAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACATTTCTGCGATACATGAGTACCCAg                   <  1:175793/71‑1 (MQ=255)
                                                     tgtgtgAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATa                                >  1:2996824/1‑57 (MQ=255)
                                                     tgtgtgAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAg                   >  1:127368/1‑70 (MQ=255)
                                                       tgtgAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAAc                <  1:3560637/71‑1 (MQ=255)
                                                       tgtgAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAAc                <  1:1928890/71‑1 (MQ=255)
                                                         tgAGAAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAAcc               <  1:2592461/70‑1 (MQ=255)
                                                          gagaAGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTg             >  1:2547287/1‑71 (MQ=255)
                                                            gaAGTCGAAACTCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTGgc           >  1:2843306/1‑71 (MQ=255)
                                                             aaGTCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTGgcg          <  1:3499084/71‑1 (MQ=255)
                                                                tCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGa                  <  1:1123372/60‑1 (MQ=255)
                                                                tCGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCt              <  1:2267102/64‑1 (MQ=255)
                                                                 cGAAACGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTGgcgcagc      >  1:1388789/1‑71 (MQ=255)
                                                                     gcgcAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTGGcgcagcgcag  >  1:2645263/1‑71 (MQ=255)
                                                                     |                                                                      
TGTGTTCACCAGGTCTTCGACCGCACGAATCTCTTCTGGTTTCATCGCTTCGTTGTGTGAGAAGTCGAAGCGCAGCACCTTGTCGTTAACCAGTGAACCTTTCTGCGATACATGAGTACCCAGAACCTGGCGCAGCGCAG  >  minE/1813323‑1813462

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