Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,637,646	+T	coding (5/1500 nt)	pitA →	metal phosphate:H(+) symporter PitA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,637,645	1	.	T	93.1%	70.3 / 0.1	29	coding (4/1500 nt)	pitA	metal phosphate:H(+) symporter PitA
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base T (11/16);  total (11/18)
Fisher's exact test for biased strand distribution p-value = 5.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01

AATTATATAAGATAATTATTTTTTGAGTGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGC‑T‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCAACCGTTATCTATACCCGCGC  >  NC_000913/3637504‑3637781                                                                                                                                               |                                                                                                                                          aaTTATATAAGATAATTATTTTTTGAGTGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCCCAAAATAGCGTAACGTCCTACGC‑t                                                                                                                                          >  2:715646/1‑143 (MQ=255)      tataAGATAATTATTTTTTGAGTGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGC‑ttacat                                                                                                                                     >  1:84006/1‑138 (MQ=255)      tataAGATAATTATTTTTTGAGTGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGC‑ttacat                                                                                                                                     <  1:507883/143‑6 (MQ=255)              aaTTATTTTTTGAGTGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCAGCGTTCATGTCCTCAAAATGGCGTAACGTGCTATGCTT‑ACAtttgtttgt                                                                                                                             >  1:679595/1‑142 (MQ=255)                            tGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATTATGCGCCGCTTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGc                                                                                                               <  1:113036/143‑1 (MQ=255)                              aaaTCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCAt                                                                                                             >  2:759565/1‑143 (MQ=255)                                    aTACAGGGGGCAAATCAAAAAAAGTCTATATTTCACGTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCggg                                                                                                       >  1:516910/1‑143 (MQ=255)                                        aGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGt                                                                                                   >  1:263439/1‑143 (MQ=255)                                                       aaaaGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCAc                                                                                    <  2:25454/143‑1 (MQ=255)                                                         aaGTCTATATTTCAGTCTGCCCTCTCCGCGAAAGTCACTGGTAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTg                                                                                  <  2:124595/143‑1 (MQ=255)                                                            tCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGCTAATGCGCCGCGTTCATGTCCTCAACATGGCGTAACGTCCTATGCTT‑ACATTTGCTTGCTGGCCTGCATCTGCATACCGGGCTGTTCTTATTGCTTGCACTCGCt                                                                               >  2:486120/1‑143 (MQ=255)                                                               tgatTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTGCATGTCCGCAAAATGGCGTAACGTCCTATGC‑T‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTtg                                                                           <  2:28738/141‑1 (MQ=255)                                                               atacTTCACTGTGCCCGCGCCGCGAAAGTCACTGATCATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCtttt                                                                            <  2:527711/143‑1 (MQ=255)                                                                  tttCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCCTGCCCTGTCTTTtctg                                                                         >  2:160736/1‑143 (MQ=255)                                                                  tttCACTGTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTtgtg                                                                         <  2:467656/143‑1 (MQ=255)                                                                    gcccTTTGCCCGCGCCGCGAAAGTCACTGGTGATGCGCCGCGTTCATGTCCTCAAAATGGCGTGACGTCCTATGCTT‑ACGTTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCt                                                                       <  2:481034/140‑1 (MQ=255)                                                                              cgcgccgcgAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACACTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGaa                                                             <  1:304735/143‑1 (MQ=255)                                                                                cgccgcgAAAGTCTCTGATGATGCGCCGCGTTCAGGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACAGTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGc                                                           <  1:191186/143‑1 (MQ=255)                                                                                   cgcgAAAGTCACTGATAATGCGCCGCTTTTATGTCCTCAATTTTGCGTATCTTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGGTTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCAt                                                        <  1:378331/143‑1 (MQ=255)                                                                                       atagttccTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGTCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAAt                                                    <  2:74370/136‑1 (MQ=255)                                                                                              cTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTcc                                             <  1:658221/143‑1 (MQ=255)                                                                                               tGATAATGCGCCGCGTTCATGTACTCAAAATGGCGAGTCGTCCGATTCTT‑ACATTTGTTTGCTGGCCTGGATGTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCa                                            <  1:664285/143‑1 (MQ=255)                                                                                                 aTAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCCTTTGTGCTGTTCTACGACGCCATCCCTGGTTTCCCTg                                          >  1:255781/1‑143 (MQ=255)                                                                                                   aaTGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGCAGCCATCTATGGTTTCCCTGac                                        >  2:285320/1‑143 (MQ=255)                                                                                                      gcgcCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCATGAcaca                                     <  1:759565/143‑1 (MQ=255)                                                                                                                      cTCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTTCTGTTCTACGAAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCaa                     >  1:486649/1‑143 (MQ=255)                                                                                                                       tCAAAATGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCGTGACACAGCCAACGCCGTGGCAAc                    >  1:354061/1‑143 (MQ=255)                                                                                                                             tGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGTATTTGCATACCGGGCTGTTATTATGGCTTGCACTGGCTTTTGTGCTGTTCTACGCAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCAACCGTTAt              <  2:195527/143‑1 (MQ=255)                                                                                                                             tGGCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGTAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCAACCGTTAt              <  1:298462/143‑1 (MQ=255)                                                                                                                              ggCGTAACGTCCTATGCTT‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCAACCGTTATc             <  1:160736/143‑1 (MQ=255)                                                                                                                                         cTATGCTT‑ACATTTGGTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTAGCTTATGTGCTGTTCTACGAAGCCATCAATGGTTTCCATAACACAGCCAACGCCGTCGCAACCGCTATCTCTACCcgcgc  >  2:281946/1‑143 (MQ=255)                                                                                                                                         cTATGC‑TCATATTTGTTTGCTGGCCGGCATTTGCATACCGGGCTGTTATTCTTGCTTGCCCTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCAACCGTTATCTATACCcgcgc  <  2:679595/143‑1 (MQ=255)                                                                                                                                               |                                                                                                                                          AATTATATAAGATAATTATTTTTTGAGTGAAATCCATACAGGGGGCAAATCAAAAAAAGTCTATATTTCACTTTGCCCGCGCCGCGAAAGTCACTGATAATGCGCCGCGTTCATGTCCTCAAAATGGCGTAACGTCCTATGC‑T‑ACATTTGTTTGCTGGCCTGGATTTGCATACCGGGCTGTTATTATTGCTTGCACTGGCTTTTGTGCTGTTCTACGAAGCCATCAATGGTTTCCATGACACAGCCAACGCCGTGGCAACCGTTATCTATACCCGCGC  >  NC_000913/3637504‑3637781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑