Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	938,685	T→C	V231A (GTC→GCC)	rarA →	recombination factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	938,685	0	T	C	96.0%	77.5 / ‑4.2	25	V231A (GTC→GCC)	rarA	recombination factor
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (13/11);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

CAGGATATTGTTCTGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGTCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGTCGGTACGTGGTAGCGCACCCGATG  >  NC_000913/938555‑938810                                                                                                                                   |                                                                                                                              cAGGATATTGTTCTGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGccc                                                                                                                             >  2:426535/1‑133 (MQ=255) cAGGATATTGTTCTGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGccc                                                                                                                             >  1:389303/1‑133 (MQ=255)     atatTGTTCTGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGaa                                                                                                                         <  1:54639/133‑1 (MQ=255)       atTGTTCTGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGc                                                                                                                       <  1:436175/133‑1 (MQ=255)              tGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAAtt                                                                                                                >  1:377135/1‑133 (MQ=255)                ccAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGCTAGCGGTGAGCGGGCCGTGAATCCTGAATTAc                                                                                                              >  2:216950/1‑133 (MQ=255)                ccAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTAc                                                                                                              >  1:353137/1‑133 (MQ=255)                               cgcgCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCg                                                                                               >  1:332181/1‑133 (MQ=255)                                 cgcCATTGCTGAACTGGTGAATGGGGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGt                                                                                             >  2:479927/1‑133 (MQ=255)                                  gcCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTg                                                                                            <  1:4918/133‑1 (MQ=255)                                              cTGGTGAATGGCGACGCGTGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGccc                                                                                <  1:216950/133‑1 (MQ=255)                                                  tGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCtt                                                                            <  2:305867/133‑1 (MQ=255)                                                   gAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCttt                                                                           <  1:288454/133‑1 (MQ=255)                                                                 gcCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAG‑GGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGAt                                                            <  1:94788/133‑1 (MQ=255)                                                                         ttAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCtttt                                                     <  2:332181/133‑1 (MQ=255)                                                                              tACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGTCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGAt                                                <  1:22471/133‑1 (MQ=255)                                                                                           atgGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCAc                                   >  2:117461/1‑133 (MQ=255)                                                                                           atgGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTGTGATAACAGAGGAGATCGCTTTTACCATCTCATTTCCGCAc                                   >  2:163788/1‑133 (MQ=255)                                                                                             ggCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTg                                 >  2:336259/1‑133 (MQ=255)                                                                                               cGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCa                               <  1:479927/133‑1 (MQ=255)                                                                                               cGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGAGAACAAAGGTGATCGATGCTACGATCGGATTCGCGCACTgga                               >  2:239372/1‑131 (MQ=255)                                                                                                ggATATGGCCGAAGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCAt                              >  2:451403/1‑133 (MQ=255)                                                                                                            aGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGt                          <  2:496787/125‑1 (MQ=255)                                                                                                            aGTCGATGATAGCGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGt                          >  1:496787/1‑125 (MQ=255)                                                                                                                  tgatAGCGCTAAGCGTGCTCTGCAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGTCGGTACGTGGTAgc            <  1:239372/133‑1 (MQ=255)                                                                                                                        cGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATACGTCTGTCCGTGGTTGCGCAccc      >  1:152873/1‑133 (MQ=255)                                                                                                                        cGGTAAGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGTCGGTACGTGGTAGCGCAccc      >  1:284020/1‑133 (MQ=255)                                                                                                                            aaGCGGGCCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGTCGGTACGTGGTAGCGCACCCGATg  <  1:336259/133‑1 (MQ=255)                                                                                                                                   |                                                                                                                              CAGGATATTGTTCTGCCAGATGAAACACGACGCGCCATTGCTGAACTGGTGAATGGCGACGCGCGCCGGGCGTTAAATACGCTGGAAATGATGGCGGATATGGCCGAAGTCGATGATAGCGGTAAGCGGGTCCTGAAGCCTGAATTACTGACCGAAATCGCCGGTGAACGTAGCGCCCGCTTTGATAACAAAGGCGATCGCTTTTACGATCTGATTTCCGCACTGCATAAGTCGGTACGTGGTAGCGCACCCGATG  >  NC_000913/938555‑938810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑