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 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,141,409 C→T 9.7% A79A (GCG→GCA)  hybC ← hydrogenase 2, large subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,141,4090CT 9.7% 183.2 / 8.6 62A79A (GCG→GCA) hybChydrogenase 2, large subunit
Reads supporting (aligned to +/- strand):  ref base C (26/30);  new base T (4/2);  total (30/32)
Fisher's exact test for biased strand distribution p-value = 4.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

TGGTGTGCGCAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGCCACAGATACGTTG  >  W3110S.gb/3141345‑3141474
                                                                |                                                                 
tggtgTGCGCAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACtt                                                             <  1:2277415/71‑1 (MQ=255)
    gtgCGCAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTg                                                         >  1:878322/1‑71 (MQ=255)
     tgagcAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGc                                                        >  1:1175936/4‑71 (MQ=255)
     tgCGCAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACt                                                              <  1:1691310/65‑1 (MQ=255)
       cgcAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGTGCACTTTCTGCCg                                                      >  1:2346571/1‑71 (MQ=255)
           gCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACg                                                  <  1:1372018/71‑1 (MQ=255)
                aaTGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACg                                                  <  1:2185699/66‑1 (MQ=255)
                aaTGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACg                                              >  1:2543725/1‑70 (MQ=255)
                aaTGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACg                                              >  1:1540222/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:2143414/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:1829861/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:1755395/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:259719/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:2044723/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:523136/1‑70 (MQ=255)
                 atgatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             >  1:1425433/1‑70 (MQ=255)
                   gatgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGTGCACTTTCTGCCGCACGAACgg                                             >  1:2054916/1‑68 (MQ=255)
                    atgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAgcg                                                                  >  1:2329791/1‑46 (MQ=255)
                    atgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGa                                         >  1:1167396/1‑71 (MQ=255)
                    atgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGa                                         >  1:2219261/1‑71 (MQ=255)
                    atgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAAAGGAAGa                                         <  1:214666/71‑1 (MQ=255)
                    atgTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTAAgcg                                                                  >  1:2734827/1‑46 (MQ=255)
                      gTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGTGCACTTTCTGCCGCACGAACGGAAGa                                         >  1:1743156/1‑69 (MQ=255)
                       ttACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACa                                       <  1:893137/70‑1 (MQ=255)
                       ttACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAg                                      >  1:646873/1‑71 (MQ=255)
                       ttACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAg                                      <  1:25517/71‑1 (MQ=255)
                       ttACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAg                                      <  1:1785036/71‑1 (MQ=255)
                        tACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAgc                                     >  1:1681254/1‑71 (MQ=255)
                         aCGGATGTATTGCGTGTTAACCGGAACGTCGATATTCAGCGCAc                                                               >  1:2407583/1‑44 (MQ=255)
                         aCGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGAc                                        >  1:957034/1‑67 (MQ=255)
                         aCGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAgc                                     >  1:1702167/1‑70 (MQ=255)
                         aCGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAgc                                     >  1:577553/1‑70 (MQ=255)
                            gATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCC‑CACGAACGGAAGACAGCGCGTg                                <  1:974801/71‑1 (MQ=255)
                             aTGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACgg                                             <  1:345987/58‑1 (MQ=255)
                             aTGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTg                                <  1:1833583/71‑1 (MQ=255)
                             aTGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTg                                <  1:2548495/71‑1 (MQ=255)
                             aTGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTg                                <  1:1239694/71‑1 (MQ=255)
                             aTGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTg                                <  1:441585/71‑1 (MQ=255)
                                tATTGCGCGTTAACCGGAACGTCGATATTCAGTGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAg                              <  1:1043926/70‑1 (MQ=255)
                                tATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAg                              <  1:1228885/70‑1 (MQ=255)
                                  ttGCGCGTTAACCGGAACGTCGATATTCAGTGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTgg                           <  1:1375143/71‑1 (MQ=255)
                                  ttGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAAc                                               >  1:1033619/1‑51 (MQ=255)
                                  ttGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGaa                                           <  1:2430293/55‑1 (MQ=255)
                                  ttGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGt                             <  1:1651976/69‑1 (MQ=255)
                                  ttGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTgg                           >  1:1264338/1‑71 (MQ=255)
                                  ttGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTgg                           >  1:2710099/1‑71 (MQ=255)
                                    gcgcGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGaa                                                >  1:1253142/1‑48 (MQ=255)
                                    gcgcGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGgt                          <  1:1031679/70‑1 (MQ=255)
                                    gcgcGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGgt                          <  1:2435352/70‑1 (MQ=255)
                                    gcgcGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGgt                          <  1:58750/70‑1 (MQ=255)
                                         ttAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGt                                 <  1:1247560/58‑1 (MQ=255)
                                         ttAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACa                    <  1:1645459/71‑1 (MQ=255)
                                         ttAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACa                    <  1:1451159/71‑1 (MQ=255)
                                           aaCCGGAACGTCGATATTCAGTGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATa                  >  1:1887482/1‑71 (MQ=255)
                                                  aCGTCGATATTCAGCGCACTTTCTGCCGCACGAAGGGAAGACa                                       >  1:2601491/1‑43 (MQ=255)
                                                  aCGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACa                                       >  1:2024912/1‑43 (MQ=255)
                                                  aCGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGCcaca           <  1:2723328/71‑1 (MQ=255)
                                                   cGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGgtagta                      <  1:1535637/59‑1 (MQ=255)
                                                   cGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGgtagta                      <  1:1302210/59‑1 (MQ=255)
                                                     tCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGt                                 <  1:2613491/46‑1 (MQ=255)
                                                           ttCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGc               <  1:770481/58‑1 (MQ=255)
                                                           ttCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGc               <  1:2125861/58‑1 (MQ=255)
                                                           ttCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGCCACAGATACGTTg  <  1:150255/71‑1 (MQ=255)
                                                             cAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGCca             >  1:859956/1‑58 (MQ=255)
                                                                |                                                                 
TGGTGTGCGCAGCCAGAATGATGTTACGGATGTATTGCGCGTTAACCGGAACGTCGATATTCAGCGCACTTTCTGCCGCACGAACGGAAGACAGCGCGTGAGTGGTAGTACATACGCCACAGATACGTTG  >  W3110S.gb/3141345‑3141474

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