Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,461,4790GA63.4% 32.2 / 42.4 41G238S (GGT→AGT) paaH3‑hydroxybutyryl‑CoA dehydrogenase
Reads supporting (aligned to +/- strand):  ref base G (0/15);  new base A (16/10);  total (16/25)
Fisher's exact test for biased strand distribution p-value = 5.42e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.37e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ATTGACGCTGCACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGTTT  >  W3110S.gb/1461413‑1461517
                                                                  |                                      
aTTGACGCTGCACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTc                                     <  1:3995810/70‑1 (MQ=255)
aTTGACGCTGCACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTc                                     <  1:3060339/70‑1 (MQ=255)
          cACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCaa                           <  1:632306/70‑1 (MQ=255)
          cACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCaa                           <  1:3503183/70‑1 (MQ=255)
          cACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCaa                           <  1:1819646/70‑1 (MQ=255)
                  gATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTc                             >  1:2938220/1‑60 (MQ=255)
                  gATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGt                  >  1:990207/1‑71 (MQ=255)
                  gATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGt                  >  1:407851/1‑71 (MQ=255)
                  gATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGt                  >  1:2406815/1‑71 (MQ=255)
                  gATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGt                  >  1:2095295/1‑71 (MQ=255)
                  gATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGt                  >  1:1820870/1‑71 (MQ=255)
                   aTGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGTc                 <  1:58018/71‑1 (MQ=255)
                            gTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTc         <  1:2001630/70‑1 (MQ=255)
                            gTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTc         <  1:3214129/70‑1 (MQ=255)
                            gTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTc         <  1:665700/70‑1 (MQ=255)
                            gTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTc         <  1:3112498/70‑1 (MQ=255)
                            gTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTc         <  1:489518/70‑1 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:3743655/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:1645802/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:3103052/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:3029742/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:2762888/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:2750896/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:2693151/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:858420/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGttt  >  1:1035889/1‑70 (MQ=255)
                                   gATGGGGCCGCTGGAATTAACCGATCTGATTAGTCAGGACCTCAATTTTGCTGTCACCTGTTCGGAGttt  >  1:3715064/1‑70 (MQ=255)
                                                   ttAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGt                  <  1:43429/38‑1 (MQ=255)
                                                   ttAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGt                  <  1:1214500/38‑1 (MQ=255)
                                                   ttAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGt                  <  1:1239312/38‑1 (MQ=255)
                                                   ttAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGt                  <  1:3169515/38‑1 (MQ=255)
                                                   ttAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGt                  <  1:1866465/38‑1 (MQ=255)
                                                   ttAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGt                  <  1:1878243/38‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:3443967/42‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:1869481/42‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:1748896/42‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:1812843/42‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:2518346/42‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:626144/42‑1 (MQ=255)
                                                          aTCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:1077889/42‑1 (MQ=255)
                                                          aTCTGATTGCTCAGGACGTCAATTTTGCTGTCACCTGTTCgg       <  1:2047981/42‑1 (MQ=255)
                                                                  |                                      
ATTGACGCTGCACTTCGCGATGGCGCTGGTTTCCCGATGGGGCCGCTGGAATTAACCGATCTGATTGGTCAGGACGTCAATTTTGCTGTCACCTGTTCGGTGTTT  >  W3110S.gb/1461413‑1461517

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: