Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,857,146	0	C	G	38.9%	59.7 / 72.7	54	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base C (14/19);  new base G (16/5);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 2.41e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑AT‑C‑TCAGGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCT  >  NC_000913/2857026‑2857244                                                                                                                            |                                                                                                   tATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCAt                                                                                  >  1:1231726/1‑139 (MQ=255)     tgATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCg                                                                              <  2:1231726/139‑1 (MQ=255)         tACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACTCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGAt                                                                          >  2:876112/1‑139 (MQ=255)            aaCGAAACTAAAAACCATCACACCGCATTTAATATCAGGGTACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATctg                                                                       >  2:1020272/1‑137 (MQ=255)             aCGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATccgg                                                                      >  1:1542797/1‑137 (MQ=255)             aCGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCctg                                                                      >  1:703154/1‑139 (MQ=255)                             tCACACCCCATTTAATATCACGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTACTGTTTTACCGGATgg                                                      >  2:1134138/1‑139 (MQ=255)                                   cccATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCctgctg                                                                   <  2:700692/120‑1 (MQ=255)                                   cccATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCctgctg                                                                   >  1:700692/1‑120 (MQ=255)                                       tttAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCAGCTGTTTTACCGGATGGGTGATTTTTa                                            >  1:722796/1‑139 (MQ=255)                                           atatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        <  2:1542797/139‑1 (MQ=255)                                            tatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       <  2:722796/139‑1 (MQ=255)                                            tatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       <  1:1134138/139‑1 (MQ=255)                                             atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctg                                                                      <  2:1414282/107‑1 (MQ=255)                                             atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctg                                                                      >  1:1414282/1‑107 (MQ=255)                                               cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       <  1:324728/136‑1 (MQ=255)                                               cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       >  2:324728/1‑136 (MQ=255)                                                      ccGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCgg                                                          <  2:1270313/110‑1 (MQ=255)                                                      ccGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCgg                                                          >  1:1270313/1‑110 (MQ=255)                                                         gACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATgacga                          >  1:18218/1‑139 (MQ=255)                                                          aCATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       <  2:946472/125‑1 (MQ=255)                                                          aCATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       >  1:946472/1‑125 (MQ=255)                                                                  ccATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcg                 <  2:18218/139‑1 (MQ=255)                                                                   cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGa                                                  <  1:1374507/105‑1 (MQ=255)                                                                   cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcgc                >  1:1425898/1‑139 (MQ=255)                                                                   cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcg                 <  1:1522561/138‑1 (MQ=255)                                                                   cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGa                                                  >  2:1374507/1‑105 (MQ=255)                                                                   cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcg                 >  2:1522561/1‑138 (MQ=255)                                                                    aTGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcgcg               >  2:117735/1‑139 (MQ=255)                                                                    aTGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcgcg               >  1:1227684/1‑139 (MQ=255)                                                                     tGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGt                                                    >  2:1000901/1‑101 (MQ=255)                                                                     tGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGt                                                    <  1:1000901/101‑1 (MQ=255)                                                                        gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        <  2:693646/110‑1 (MQ=255)                                                                        gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        >  1:693646/1‑110 (MQ=255)                                                                         tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        <  1:685284/109‑1 (MQ=255)                                                                         tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        >  2:685284/1‑109 (MQ=255)                                                                         tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCg          >  1:1253452/1‑139 (MQ=255)                                                                          gCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGc         <  2:1425898/139‑1 (MQ=255)                                                                           cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        <  2:990464/107‑1 (MQ=255)                                                                           cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       <  2:88019/108‑1 (MQ=255)                                                                           cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                        >  1:990464/1‑107 (MQ=255)                                                                           cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                       >  1:88019/1‑108 (MQ=255)                                                                           cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCa        >  2:532433/1‑139 (MQ=255)                                                                             aTAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctg                                                                      >  2:252316/1‑75 (MQ=255)                                                                             aTAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctg                                                                      <  1:252316/75‑1 (MQ=255)                                                                              tAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAAct     >  2:144863/1‑139 (MQ=255)                                                                               aGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActg    <  2:703154/139‑1 (MQ=255)                                                                                 aaaaTTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct  <  2:1253452/139‑1 (MQ=255)                                                                                      ttCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGc         <  1:1260649/127‑1 (MQ=255)                                                                                      ttCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGc         >  2:1260649/1‑127 (MQ=255)                                                                                          acgcccatacgcccatGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCg                                                                              <  2:490701/54‑1 (MQ=255)                                                                                          acgcccatacgcccatGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCg                                                                              >  1:490701/1‑54 (MQ=255)                                                                                                atacgcccatGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctgct                                                                    <  2:455548/58‑1 (MQ=255)                                                                                                atacgcccatGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctgct                                                                    >  1:455548/1‑58 (MQ=255)                                                                                                                            |                                                                                                   TATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑AT‑C‑TCAGGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCT  >  NC_000913/2857026‑2857244

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑