Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	73,581	0	A	C	50.0%	56.9 / 13.8	48	V314G (GTA→GGA)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base A (18/6);  new base C (1/23);  total (19/29)
Fisher's exact test for biased strand distribution p-value = 5.67e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATG  >  NC_000913/73438‑73721                                                                                                                                                 |                                                                                                                                             gcgcCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATc                                                                                                                                       >  1:147244/1‑151 (MQ=255) gcgcCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATc                                                                                                                                       >  1:272615/1‑151 (MQ=255)     ccGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATcgacg                                                                                                                                   <  1:393980/151‑1 (MQ=255)       gCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGAt                                                                                                                                 <  1:668435/151‑1 (MQ=255)        cAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATc                                                                                                                                >  2:176404/1‑151 (MQ=255)                  cTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGt                                                                                                                       >  2:385156/1‑150 (MQ=255)                        cATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTg                                                                                                                >  2:244215/1‑151 (MQ=255)                         aTAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTgg                                                                                                               >  1:576915/1‑151 (MQ=255)                         aTAGCAGAATCAGGGTCAGCACTCCGCACAACCCCCCTGCCCCCAGCGCAATACGCACGGAGGCCCCCAGCGCCGGCCACAGCCCC‑GGTTGGCCCAGCCCTGCCGGCAAGTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTgg                                                                                                               <  2:177083/151‑1 (MQ=255)                            gcagcaTCAGGGTCACCACTCCGCAAAATCCCCCTGCCGCCAGCGCAATACGCAATGAGGCCCACAGCGCCTGCCACAGCCCG‑GGTTGGGCCAGCCCTTCCGGCAACGGGCGTTTTCCCCCATCGACGATCACCGCCAGTAACGGTGgca                                                                                                             <  2:182623/150‑1 (MQ=255)                                catcatGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAAc                                                                                                        >  2:526654/1‑151 (MQ=255)                                catcatGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAAc                                                                                                        >  1:101717/1‑151 (MQ=255)                                      ggTCACCACCCCACAAAATCCCCCTCCCGCCAGCGCAATACGCAACGGGGCCCACGGCGCCGCCCACGCCCCC‑GGTGGGGCCAGCACTCCGGGCACGGGGCGATTTCCCCAACCGACGATCACCGCCAGTAACGGTGGCAGCAAcagc                                                                                                     <  2:5175/148‑1 (MQ=255)                                         cAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACagcagcagc                                                                                               >  1:534334/1‑151 (MQ=255)                                            cACTACGCAAAATCCCCCCGCCGCCAGCGCAATACGCAACGAGGCCCCCAGCGCCTGCCACACCACC‑GTTTGGGCCAGCACTCCCGGCAACGGGCGATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAgcg                                                                                              <  1:583833/149‑1 (MQ=255)                                               tACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGc                                                                                         >  1:650898/1‑151 (MQ=255)                                                 cgcccaaacccccTGCCGCCAGCGCAATACGCAACGAGGCCCCCGCCCCCTGCCACACCACC‑GGTTGGGCCAGCCCTCCCGGCAACGGGCGATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGca                                                                                        <  2:460522/139‑1 (MQ=255)                                                 ccaacaATCCCCCCGCCCCCGGCGAAATACGCAACGGGGCCCACCGCCCCTGCCCCAGCCCC‑GTTGGTGCCAGCCCTCCCGGCAAGTGGCGATTTCCCCCATCGCCGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGcac                                                                                       <  2:477368/148‑1 (MQ=255)                                                 cGCAAAATCCCCCTGCCGCCAGCGAAATCCGAAACGAGTTCCACAGCGCCTGCCACAGCCCC‑GGTTGGGCCAGCCCTCCCGGCAACGGGCGATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAgcgc                                                                                             <  1:411774/145‑1 (MQ=255)                                                     caATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAAtt                                                                                   >  1:477357/1‑151 (MQ=255)                                                        tACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAac                                                                                >  1:405682/1‑151 (MQ=255)                                                                cccccACCGAAATACGAAACGAGGCCCACGCCGCCTGCCACAGCACC‑GGTTGCGCCACCACTTCCGGCAAGGGGAGTTTACCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTc                                                                        <  1:209566/148‑1 (MQ=255)                                                                 ccccggcgaaaaccGCAACGAGGCCCACAGCGCCTGCCACAGCCCC‑GGTTGGCCCAGCACTCCCGGAAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAATACCGTGTCg                                                                       <  1:15419/138‑1 (MQ=255)                                                                 ccccAGCGCAATACGCAACGAGGCCCACAGCCCCGCCCACAGCACC‑GGTTGTCCCACCTCTGCCGGCAACGGGCGATTTCCCCCATCGACGACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCg                                                                       <  2:344419/149‑1 (MQ=255)                                                                            tACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCt                                                            >  2:486121/1‑151 (MQ=255)                                                                                   cGAGGTCCACAGCCCCTGCCACAGCACC‑GGTTGTCCCAGCTCTCCCGGCAACGGGCGATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAg                                                      <  1:691400/150‑1 (MQ=255)                                                                                    gagcccccagccgcCTGCCCCGGCGCC‑GGTTGGCCCACCCCTTCCGCCAGCGGGCGATTTCCCCCAGCGCCGACACCCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGc                                                        <  2:205216/136‑1 (MQ=255)                                                                                    gAGGTCCACGCCCCCGGCCA‑AGCCCCGGGTGGTGCAAGCATTTCCGGCAACGGGCGATTCACCCCAGCGGCGACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGAAg                                                      <  2:578992/149‑1 (MQ=255)                                                                                    gAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAg                                                      >  2:532465/1‑149 (MQ=255)                                                                                    gAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGAc                                                    >  2:343931/1‑151 (MQ=255)                                                                                    gAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTACCCCCATCGCGGGCGCCCGCAAGTAACGGTGCCGGCACCACCAGAGCCGCAACAACATTTAACACGGTGCGGCAAAggcggcatt                                                          >  2:675950/1‑142 (MQ=255)                                                                                         ccACCGCCCCAGCCACGCCCCG‑GGTGGGGCCAGCCCTCCCGGAACGGGGCGTTTTCCCCCACCGACAACCCCCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATc                                                <  2:545583/150‑1 (MQ=255)                                                                                               cgccgcccACAGCACG‑GGTTGGGCCAGCACTCCCGGCAACTGGCGATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGt                                              <  1:605591/140‑1 (MQ=255)                                                                                               cgcCTGCCACAGCCCC‑GTTTGGGCCAGCACTTCCGGCAACTGGCGTTTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGt                                              <  1:372182/146‑1 (MQ=255)                                                                                                     ccACGGCACG‑GGTTGGCCCAGCCCTCCCGGAACCGGGCGATTTCCCCCACCGACAATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTc                                       <  2:270596/147‑1 (MQ=255)                                                                                                       acaGCCCC‑GGTTGGGCCAGCCCTCCCGGCAACGGGGGATTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCa                                 <  1:174014/151‑1 (MQ=255)                                                                                                        caGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGcc                                  >  1:514655/1‑149 (MQ=255)                                                                                                           cACC‑GGTGGTGCCAGCACTTCCGGCAACGGGCGATTTCCCCCAGCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAg                                <  2:471791/148‑1 (MQ=255)                                                                                                              cggtttGTCCCACCCCTTCCGGCAACTGGCGATTTACCCCATCAACAATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCtt                            <  1:170478/146‑1 (MQ=255)                                                                                                                    gtgCCAGCACTTCCGGCAACGGGCGTTTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTgcagc                       <  1:687816/149‑1 (MQ=255)                                                                                                                      gCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCg                   >  2:391277/1‑151 (MQ=255)                                                                                                                       ccacccctcccGGCACCGGGCGATTTCCCCCATCGCCGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCgt                  <  1:224987/142‑1 (MQ=255)                                                                                                                       ccAGCCCTCCCGGCACCTGGCGTTTTCCCCCATCGACGACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCgt                  <  1:86311/151‑1 (MQ=255)                                                                                                                                ccGCCAACGGGCGATTTCCCCCATCGACAACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCgg          <  2:686629/150‑1 (MQ=255)                                                                                                                                  ggCAACTGGCGATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGgc        <  1:644762/150‑1 (MQ=255)                                                                                                                                  gcaaacggccGATTCCCCCCAGCGCCAACCCCCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCgtggtg              <  2:484355/135‑1 (MQ=255)                                                                                                                                    cAACTGGCGATTCCCCCCACCGACGACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCa     <  2:147231/151‑1 (MQ=255)                                                                                                                                       cTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATg  >  1:98852/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                             GCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC‑GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATG  >  NC_000913/73438‑73721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑