Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,431	0	A	C	41.5%	62.2 / 12.8	43	G34G (GGT→GGG)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base A (19/5);  new base C (1/16);  total (20/23)
Fisher's exact test for biased strand distribution p-value = 3.40e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

GGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGAC  >  NC_000913/2248284‑2248578                                                                                                                                                      |                                                                                                                                                    ggCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCt                                                                                                                                                  <  2:119582/151‑1 (MQ=255)   cAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGTCAGAGG‑CAACAAAAAGACCTGt                                                                                                                                                <  1:239626/151‑1 (MQ=255)    aaaCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGt                                                                                                                                                >  2:77487/1‑150 (MQ=255)       cGAACCGAAAACCGGCATATATGCAACCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGGCCTGTTCCg                                                                                                                                            <  1:117074/151‑1 (MQ=255)            cGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATgg                                                                                                                                        >  2:68604/1‑150 (MQ=255)             ggAAACCGGCATATATGCAGCCAGTTCACCCAGACTGGTACTCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCCGCCTCAGAAATCGTCGCGTCAGAGG‑CAACAAAAAGCCCTGTACCGAt                                                                                                                                          >  1:240754/1‑147 (MQ=255)              gAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAAc                                                                                                                                     <  1:701991/151‑1 (MQ=255)               aaaCCGGCATATATGCAGCCAGTTCACCAATAGTGGTCAGCAGGAAGTAAACCCTCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGTCCTGTACCGATGGa                                                                                                                                       <  1:144932/148‑1 (MQ=255)                      cATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTCCCGATGGAACCGCCa                                                                                                                                <  1:160454/148‑1 (MQ=255)                         atatGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGGACCGATGGCACCGCCAATGGc                                                                                                                           >  2:799847/1‑150 (MQ=255)                             gCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAatc                                                                                                                       >  1:330371/1‑150 (MQ=255)                              cAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAACAGACCTGTACCGATGGAACCGCCAATGGCAatca                                                                                                                      >  1:446264/1‑150 (MQ=255)                                     ttCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAgg                                                                                                              >  2:130977/1‑151 (MQ=255)                                            agaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                                       >  2:724715/1‑151 (MQ=255)                                               aggtacaccaGGAACTAACCCACCAGCCAAATCAGCATCAGCGAGAG‑CATAGCCCCCCCCAGACCCGCATGA‑AAATTGCTGCCCCGAAGGACAAAAAAAATCCTTTTCCCAATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                                    <  2:282230/143‑1 (MQ=255)                                                 gttaaagaGGAAGTAAACCATCAGGCAACACAGCATAAACGAGAG‑CAATCCCCCCCCGGCCCCTCCCTGAAAAATCTTTGCGCCAGAGG‑AAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCtt                                                                                                   <  1:546251/143‑1 (MQ=255)                                                 ggTCATCAGGAAGTAAACCATCAGCCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGCCCTGCCTGAGAAATCGTTGCGCCAGAGG‑AAAAAAAAAGCCCTGTACGGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                                    <  2:167751/149‑1 (MQ=255)                                                  gTCATCAGGAAGAAACCCACCAGGCAAACAAGAATAAAGGAGAG‑AACTCCCCCGCCCGGACCTGCCGAAAAAATCGTTGCGCCAGAGG‑CAAAAAAAAGCCCTGTCCCGATGGACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTa                                                                                                 <  1:386221/151‑1 (MQ=255)                                                  gTCATCAGGAAGAAACCAACCAGCCCAACCACAATATCCGAGAC‑CAATCCCCCGCCCGGCCCTGCCTGAAAAATCGTTGCCCCAGAGG‑CAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTa                                                                                                 <  2:590771/151‑1 (MQ=255)                                                      tcaGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGCGACGCGCCTTTAATTc                                                                                             >  2:72103/1‑151 (MQ=255)                                                       caGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTc                                                                                             >  1:732460/1‑150 (MQ=255)                                                           aaGAAACCCAACAGGCCAATCAGTATA‑ACGAGGGACACCCCCCCGCCCGGCCCTGCCTGAGAATCGGTGGCGCGAGAGG‑AAAAAAAAAGCCCTGTACGGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAAt                                                                                               <  1:363357/144‑1 (MQ=255)                                                            aGTAAACCACCAGCCCAATCAGCATAACCGAGGG‑CAGCGCCCCGCCGGGCCCGGCCTGAAAAACGTTTGCGCCAGAGG‑CAAAAAAAACCCTTGTCCGGGTGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCg                                                                                       <  1:60014/151‑1 (MQ=255)                                                               aaaCAACCAGGCCAATCACCATATACGAAAG‑CAACGCCCCGCCCGGCCCTGCCGGAAAAATCGTTGCGCAAGAGA‑CAAAAAAAAGCCCTGTACCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTaa                                                                                    <  2:374088/151‑1 (MQ=255)                                                                aaCCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTa                                                                                     >  2:467904/1‑149 (MQ=255)                                                                      cAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGgc                                                                             >  2:339886/1‑151 (MQ=255)                                                                               cAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCtgtg                                                                    >  2:343258/1‑151 (MQ=255)                                                                                    aaacagagaG‑CAAGCCCCCCCCCGGCCCTGCCTGAAAATTCGTTGCGCCGGAGC‑CAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtttt                                                               <  1:23667/146‑1 (MQ=255)                                                                                     ataCGAGAG‑AAACCCCCCCCCCGGCCCTGCCGGAAAAATCGTTGCGCCAGAGG‑CAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtttt                                                               <  2:209448/150‑1 (MQ=255)                                                                                         gagaG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                          >  2:237639/1‑151 (MQ=255)                                                                                         gagaG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                          >  2:36070/1‑151 (MQ=255)                                                                                               caaccccccGCCCGACCCTCCCGGAGAAATCGTTGCGCAAGAGG‑AAAAAAAAAGCCCTTTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGaa                                                     <  1:266962/146‑1 (MQ=255)                                                                                               cAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGa                                                      >  1:745983/1‑150 (MQ=255)                                                                                                 aTGCCCCGCCCGGCCCTGCCAGAGAAATCGTGGCGCAAGAGC‑AAAAAAAAAGCCCTGCCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGaaa                                                    <  1:467800/150‑1 (MQ=255)                                                                                                    ccccGCCCGGCCCTGCCTGAGAAATCGTTGCGCCAGAGC‑CAACAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAAcc                                                  <  2:586547/149‑1 (MQ=255)                                                                                                    caccgcccgGACCTTCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGTTGGAACCGACAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCa                                                 >  1:749737/3‑150 (MQ=255)                                                                                                         cccgGCCCTGCCTGAGAAATCGTTGCGCAAGAGC‑CAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaa                                            <  2:156278/150‑1 (MQ=255)                                                                                                         cccgGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCAAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACa                                             >  1:192077/1‑149 (MQ=255)                                                                                                                        gaAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                            >  2:269300/1‑151 (MQ=255)                                                                                                                        gaAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                            >  2:126689/1‑151 (MQ=255)                                                                                                                         aagtCGTTGCGCGGGAGG‑AAAAAAAAGGACCGGTACCGGGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATg                                       <  2:322218/136‑1 (MQ=255)                                                                                                                              gTTGCGCAAGAGG‑CAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaaaa                       <  2:5894/150‑1 (MQ=255)                                                                                                                                                   aaGCCCTGTCCCAAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGAc  <  1:229375/151‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGG‑CAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGAC  >  NC_000913/2248284‑2248578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑