Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,354,024	A→G	13.3%	H90R (CAC→CGC)	PP_2949 →	permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,354,024	0	A	G	13.3%	69.6 / 2.6	30	H90R (CAC→CGC)	PP_2949	permease
Reads supporting (aligned to +/- strand):  ref base A (13/13);  new base G (2/2);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAATTGCCGCCATGCTGGGCGCACTTTTTCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGTTGGTCGCTGGCTAT  >  NC_002947/3353882‑3354166                                                                                                                                               |                                                                                                                                                acaaTTGCCGCCATGCTGGGCGCACTTTTTCTGATCGTGCTACGGCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCACTTCAGCACATAAg                                                                                                                                           <  5:134515/149‑1 (MQ=255) acaaTTGCCGCCATGCTGGGCGCACTTTTTCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAg                                                                                                                                           <  3:124048/149‑1 (MQ=255)       gccgccATGCTGGGCGCACTTTTTCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTg                                                                                                                                      <  3:173431/148‑1 (MQ=255)        ccgccATGCTGGGCGCACTTTTTCTGATCGTGCTAAGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGTTTTCCCTCTACTGACAGCATTTACCCTTCAGCACATAATCTCTGCt                                                                                                                                    >  8:162827/1‑149 (MQ=255)                   ggCGCACTTTTTCTGATCTTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCTCCTTTGTCTGTAACTTCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCAt                                                                                                                            <  7:162827/146‑1 (MQ=255)                    gcgcACTTTTTCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGtt                                                                                                                        <  5:94029/149‑1 (MQ=255)                              tCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTg                                                                                                                                      >  4:228894/1‑125 (MQ=255)                              tCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTg                                                                                                                                      <  3:228894/125‑1 (MQ=255)                                     gTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCGCATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGc                                                                                                        >  2:26150/1‑148 (MQ=255)                                        cTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAt‑t                                                                                                   <  6:51401/149‑1 (MQ=255)                                                          aaaCGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTAGTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGc                                                                                 >  1:104189/1‑149 (MQ=255)                                                          aaaCGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCGCATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGc                                                                                 <  1:26150/149‑1 (MQ=255)                                                                    aTTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCgg                                                                       <  5:123776/149‑1 (MQ=255)                                                                             cTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCGCATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCg                                                                                           >  5:233906/1‑120 (MQ=255)                                                                             cTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCGCATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCg                                                                                           <  6:233906/120‑1 (MQ=255)                                                                                  gCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGAc                                                          <  1:229161/148‑1 (MQ=255)                                                                                    tGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTc                                                       >  7:87004/1‑149 (MQ=255)                                                                                          tGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCAt                                                 >  2:77583/1‑149 (MQ=255)                                                                                               tCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTc                                            >  8:149360/1‑149 (MQ=255)                                                                                                 ggCGTTGTTATCGGTTTCCCGCTATTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCt                                           <  2:104189/148‑1 (MQ=255)                                                                                                 ggCGTTGTTATCGGGTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCGCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCATATGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCt                                           <  1:238660/149‑1 (MQ=255)                                                                                                          aTCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTtctc                                 >  7:48563/1‑149 (MQ=255)                                                                                                                        aCTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTgg                                         >  8:218076/1‑127 (MQ=255)                                                                                                                        aCTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTgg                                         <  7:218076/127‑1 (MQ=255)                                                                                                                         cTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCgg                  >  1:16433/1‑149 (MQ=255)                                                                                                                           gACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGAAGGATTTGCGGTTCTGCGGGGCGTTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGt                >  5:125790/1‑149 (MQ=255)                                                                                                                            aCAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGtt               >  1:236368/1‑149 (MQ=255)                                                                                                                            aCAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGt                <  7:149360/148‑1 (MQ=255)                                                                                                                                  tttGCCCTTCAGCACATAAGCTCTGCTCCCTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGTTGGTCGc         >  6:248276/1‑149 (MQ=255)                                                                                                                                         ttCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGTTGGTCGCTGGCTAt  >  2:69426/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                ACAATTGCCGCCATGCTGGGCGCACTTTTTCTGATCGTGCTACGCCAGCCTCGACCCAAACGGCGGGATTTGTCGCCTTTGGCTGTAACTGCGCTCGGCGTTGTTATCGGTTTCCCGCTACTGACAGCATTTGCCCTTCAGCACATAAGCTCTGCTCACTCCATTGTTTTTGTCGGGCTCCTGCCAT‑TGTGTACCGCAGGATTTGCGGTTCTGCGGGGCGGTGAACGACCTCGGCCATTGTTCTGGCTGTTCTCGTTGACAGGTGCCGGGTTGGTCGCTGGCTAT  >  NC_002947/3353882‑3354166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑