Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	155,349	0	A	C	34.7%	45.7 / 54.6	49	T26T (ACT→ACG)	htrE	putative outer membrane usher protein
Reads supporting (aligned to +/- strand):  ref base A (18/14);  new base C (9/8);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01

AGCGGGGTTACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTCCTGCGGAAT  >  NC_000913/155250‑155445                                                                                                    |                                                                                                 aGCGGGGTTACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCa                                                                                                  >  2:828377/1‑100 (MQ=255) aGCGGGGTTACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCa                                                                                                  <  2:313838/100‑1 (MQ=255)     gggTTACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTAt                                                                                              <  1:1264027/100‑1 (MQ=255)         tACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCa                                                                                          >  1:394229/1‑100 (MQ=255)         tACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGc                                                                                           <  2:1080886/99‑1 (MQ=255)             ttCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATAc                                                                                      <  1:1133207/100‑1 (MQ=255)             ttCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATAc                                                                                      <  2:529927/100‑1 (MQ=255)             ttCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATat                                                                                      >  2:1186474/1‑99 (MQ=255)             ttCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATAc                                                                                      <  1:286253/100‑1 (MQ=255)              tCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATAca                                                                                     >  2:1133197/1‑100 (MQ=255)                  tGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATAcagaag                                                                                 >  1:453542/1‑100 (MQ=255)                    tACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAgcg                                                                               <  1:725335/100‑1 (MQ=255)                           tGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCaaaa                                                                        <  1:1150694/100‑1 (MQ=255)                              gaTCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGt                                                                     >  1:1143647/1‑100 (MQ=255)                                tCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTgg                                                                   >  2:751075/1‑100 (MQ=255)                                 cAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATATAGCAGCGCGCAAAACGTGGc                                                                  <  1:1186485/100‑1 (MQ=255)                                     atTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATa                                                              >  2:882916/1‑100 (MQ=255)                                      ttAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATAc                                                             <  2:198149/100‑1 (MQ=255)                                       tAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATAc                                                             <  1:95163/99‑1 (MQ=255)                                        aGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACgg                                                           >  2:1113359/1‑100 (MQ=255)                                         gATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACggg                                                          <  2:113504/100‑1 (MQ=255)                                             cATGCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAg                                                      <  2:1001673/100‑1 (MQ=255)                                                   gCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAgatgatg                                                >  1:861914/1‑100 (MQ=255)                                                    ccccATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAgatgatga                                               >  2:305136/1‑100 (MQ=255)                                                       cATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATaa                                            >  1:700537/1‑100 (MQ=255)                                                       cATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATaa                                            >  2:1057367/1‑100 (MQ=255)                                                            ggAAGGTATGGTCATATTCAACGAGTTCCGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAAttttt                                       <  2:346/100‑1 (MQ=255)                                                             gAAGGTATGGTCATATTCAACGAGTTCAGCATTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTa                                      <  1:828383/100‑1 (MQ=255)                                                             gAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTa                                      <  1:353230/100‑1 (MQ=255)                                                                  tATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGtata                                 >  1:1173898/1‑100 (MQ=255)                                                                  tATGATCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGtata                                 >  2:988723/1‑100 (MQ=255)                                                                    tGGTCATATTCAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATAtt                               <  1:305139/100‑1 (MQ=255)                                                                     ggTCATATTCAACGAGTTCAGCACTAAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGAGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTc                              <  1:844682/100‑1 (MQ=255)                                                                        cATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCtat                           <  1:381348/100‑1 (MQ=255)                                                                             tCAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCCAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCa                      >  2:1011855/1‑100 (MQ=255)                                                                             tCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCa                      >  2:546175/1‑100 (MQ=255)                                                                             tCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCa                      >  1:542574/1‑100 (MQ=255)                                                                              cAACGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCAc                     >  2:108184/1‑100 (MQ=255)                                                                                 cGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGc                   <  2:1170333/99‑1 (MQ=255)                                                                                 cGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCt                  <  2:1128765/100‑1 (MQ=255)                                                                                 cGAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCt                  >  2:695534/1‑100 (MQ=255)                                                                                 cGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCt                  >  2:1300587/1‑100 (MQ=255)                                                                                  gAGTTCAGCACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTa                 >  2:814827/1‑100 (MQ=255)                                                                                   aGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTAt                <  2:72361/100‑1 (MQ=255)                                                                                       cAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCtt            >  2:1297107/1‑100 (MQ=255)                                                                                       cAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCtt            >  2:580966/1‑100 (MQ=255)                                                                                        aGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTc           >  1:313165/1‑100 (MQ=255)                                                                                          cACTGAAAGCCGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTc           >  2:200589/1‑98 (MQ=255)                                                                                              gAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTCCTGCgg     >  2:1106630/1‑100 (MQ=255)                                                                                                aaGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTCCTGCGGaa   >  1:848109/1‑100 (MQ=255)                                                                                                 aGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTCCTGCGGAAt  <  2:1046509/100‑1 (MQ=255)                                                                                                    |                                                                                                 AGCGGGGTTACCTTCACTGTACCGGCTGAGATCAATATTAGATGCATTCTGCCCCATCAGGAAGGTATGGTCATATTCAACGAGTTCAGCACTGAAAGCAGTATTGCAATACAGCAGCGCGCAAAACGTGGCGATACGGGTCAGATGATGATAATTTTTAGTATATTCTATAGTCACGCTATGCTTCCTGCGGAAT  >  NC_000913/155250‑155445

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑