Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,846,303:1	+A	10.0%	coding (594/1377 nt)	pfeS‑II →	histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,846,303	1	.	A	10.0%	143.3 / 11.2	40	coding (594/1377 nt)	pfeS‑II	histidine kinase
Reads supporting (aligned to +/- strand):  ref base . (20/16);  new base A (2/2);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

GCCAGCACCGCTTGCTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCTGTCCCACGAAA  >  NC_002947/1846155‑1846442                                                                                                                                                      |                                                                                                                                             gCCAGCACCGCTTGCTGTGGCGCATTGTCACCAACGTCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTg                                                                                                                                               <  8:53067/149‑1 (MQ=255)  ccAGCACCGCTTGCTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑t                                                                                                                                             <  7:73806/149‑1 (MQ=255)     gCACCGCTTGCTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCgg                                                                                                                                          >  5:270270/1‑149 (MQ=255)        ccGCTTGCTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGGACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGA‑CAGCTGATCGGccc                                                                                                                                       <  5:198547/149‑1 (MQ=255)          gCTTGCTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGAGCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGc                                                                                                                                     <  3:256811/149‑1 (MQ=255)              gCTGTGGCGCATTGTCACCAACAGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCTTGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCt                                                                                                                                   <  6:9272/147‑1 (MQ=255)               cTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGa                                                                                                                                >  7:6433/1‑149 (MQ=255)                      gcATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTcgcg                                                                                                                          >  7:76257/1‑148 (MQ=255)                        aTTGTCACCAACGGCATCATCCCGGGGCTGTGCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGAGCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCAc                                                                                                                       <  5:191501/149‑1 (MQ=255)                                cAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGccc                                                                                                               >  8:50194/1‑149 (MQ=255)                                      catcatCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCAt                                                                                                          >  2:39828/1‑148 (MQ=255)                                       atcatcCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGTCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATAGCCCGGCATG‑a                                                                                                       >  7:108312/1‑149 (MQ=255)                                       atcatcCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑a                                                                                                       >  6:165619/1‑149 (MQ=255)                                            cccGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAAt                                                                                                  >  6:16876/1‑149 (MQ=255)                                                 ggCTGTTCAGCTTGCTGTTGTGTGTAGGCGTGTACCGCATGCTGATCTTGCCGGTGAACCAAGTTCGCGAGGAGGCCAATGCGTGGCGGGCCGATGAGCTT‑TCGGCCCGCCTGGACTCGCGCACCATCGCGCGGGATG‑ACGAATTGGGc                                                                                             <  8:6433/149‑1 (MQ=255)                                                    tGTTCACCTTGCTGTTGTGTGTAGGTCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATAGCCCGGCATG‑ACGAATTGGGCGaa                                                                                          <  8:108312/149‑1 (MQ=255)                                                      ttCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACt                                                                                        >  6:270848/1‑149 (MQ=255)                                                         aCCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGgc                                                                                     <  5:165619/149‑1 (MQ=255)                                                           cTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGgcgc                                                                                   <  5:270848/149‑1 (MQ=255)                                                             tGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGt                                                                                 >  7:94950/1‑149 (MQ=255)                                                             tGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGt                                                                                 >  7:104811/1‑149 (MQ=255)                                                              gCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGt                                                                                 <  1:39828/148‑1 (MQ=255)                                                                  ttgtGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCtt                                                                            >  2:154673/1‑149 (MQ=255)                                                                     tgtgtAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATGCACGAATTGGGCGAACTGGCGCGTGCCttt                                                                           <  1:157457/148‑1 (MQ=255)                                                                       tgtAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGAc                                                                        <  8:104811/148‑1 (MQ=255)                                                                           ggCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGAt                                                                   <  5:16876/149‑1 (MQ=255)                                                                                             aTCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCgg                                                         <  2:178787/141‑1 (MQ=255)                                                                                             aTCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCgg                                                         >  1:178787/1‑141 (MQ=255)                                                                                                         aaCCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTAt                                     >  1:175334/1‑149 (MQ=255)                                                                                                                    cgAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGt                          >  4:174560/1‑149 (MQ=255)                                                                                                                     gAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGtt                         >  4:155100/1‑149 (MQ=255)                                                                                                                     gAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCCCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGtt                         >  7:181958/1‑149 (MQ=255)                                                                                                                           gCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACTATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTtgctgc                    >  4:240196/1‑148 (MQ=255)                                                                                                                           gCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACTATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTtgctgc                    <  3:240196/148‑1 (MQ=255)                                                                                                                             cAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGt                          >  7:212622/1‑140 (MQ=255)                                                                                                                             cAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGt                          <  8:212622/140‑1 (MQ=255)                                                                                                                               aTGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGAc               <  7:50194/149‑1 (MQ=255)                                                                                                                                    tGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCTGTc          >  6:24197/1‑149 (MQ=255)                                                                                                                                      gCGGGCCGA‑CAGCTGATCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCt             <  6:146195/144‑1 (MQ=255)                                                                                                                                      gCGGGCCGA‑CAGCTGATCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCt             >  5:146195/1‑144 (MQ=255)                                                                                                                                      gCGGGCCGA‑CAGCTGATCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCTGTcc         >  1:7223/1‑148 (MQ=255)                                                                                                                                            cGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCTGTCCCACGaaa  <  8:94950/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                             GCCAGCACCGCTTGCTGTGGCGCATTGTCACCAACGGCATCATCCCGGGGCTGTTCACCTTGCTGTTGTGTGTAGGCCTGTACCGCATGCTGATCGTGCCGCTGAACCAACTTCGCGAGCAGGCCAATGCCTGGCGGGCCGATCAGCTG‑TCGGCCCGCCTGGACTCGCGCACCATCGCCCGGCATG‑ACGAATTGGGCGAACTGGCGCGTGCCTTTGACCAGATGGCCGAGCGGCTGCAAGGCACGGTGGCTATGCAGCAGCAGTTGCTGCGCGACCTGTCCCACGAAA  >  NC_002947/1846155‑1846442

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑