Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,874,876	A→C	10.5%	S451A (TCG→GCG) ‡	ilvA‑II ←	threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,874,876	0	A	C	10.5%	91.0 / 5.4	38	S451A (TCG→GCG) ‡	ilvA‑II	threonine deaminase
Reads supporting (aligned to +/- strand):  ref base A (18/16);  new base C (2/2);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.05e-01

GCCGGGTTTTCGGTCTCGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATGCAGCTTGGCCAATTCGTT  >  NC_002947/5874734‑5875023                                                                                                                                                 |                                                                                                                                                    gCCGGGTTTTCGGTCTCGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGTCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTc                                                                                                                                              >  1:187308/1‑150 (MQ=255)   cGGGTTTTCGGTCTCGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCa                                                                                                                                            <  2:878913/150‑1 (MQ=255)      gTTTTCGGTCTCGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAgcg                                                                                                                                         >  1:10456/1‑150 (MQ=255)              tctcGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GGCGCTGGAACATCTCGATGTTCCactaccgc                                                                                                                                     <  2:392207/147‑8 (MQ=38)              tctcGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GGCGCTGGAACATCTCGATGTTCCactaccgc                                                                                                                                     >  1:392207/1‑140 (MQ=38)               ctcGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAg                                                                                                                                >  1:87594/1‑150 (MQ=255)                   tCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCttg                                                                                                                            >  1:1094210/1‑150 (MQ=255)                   tCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCttg                                                                                                                            <  1:527784/150‑1 (MQ=255)                    cccAGTACGGGTAACCGCTCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCCACTGCCGCCAGGCCCCCACGCGCCCGTCAGCCGCGCCACGGGTCCT‑GGAG‑TGGAAGACCGAGATGTTCCAGCGCCCGCCCAGCttgt                                                                                                                           <  2:137706/150‑1 (MQ=255)                       aGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGa                                                                                                                        <  2:176073/150‑1 (MQ=255)                              gTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGTCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGtt                                                                                                                 <  2:187308/150‑1 (MQ=255)                               tAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGtt                                                                                                                 <  1:666660/149‑1 (MQ=255)                               tAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGtt                                                                                                                 >  2:666660/1‑149 (MQ=255)                                 aCCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGG‑TGCGAAAAG‑TGGAACATAGACATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGaa                                                                                                              >  1:616709/1‑150 (MQ=255)                                  ccGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAAc                                                                                                             >  2:125382/1‑150 (MQ=255)                                   cGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACa                                                                                                            <  1:854794/150‑1 (MQ=255)                                         tagCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGccc                                                                                                      <  1:296699/148‑1 (MQ=255)                                              aGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGc                                                                                                 <  2:10456/150‑1 (MQ=255)                                                    gCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCg                                                                                           <  2:87594/150‑1 (MQ=255)                                                      cGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCggg                                                                                         <  2:386365/150‑1 (MQ=255)                                                                    gTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCgca                                                                           >  1:283261/1‑150 (MQ=255)                                                                     ttCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCgcag                                                                          <  2:283261/150‑1 (MQ=255)                                                                           ctccGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCAt                                                                    >  2:196588/1‑150 (MQ=255)                                                                                  aCCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTtcgtcg                                                             >  2:1149816/1‑150 (MQ=255)                                                                                   ccTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCCGGGAATTCGAAGCGCAGCACCATTTCGTCGc                                                            >  1:920733/1‑150 (MQ=255)                                                                                      gCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTgg                                                         >  2:1196789/1‑150 (MQ=255)                                                                                            ccGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCgg                                                   >  1:227366/1‑150 (MQ=255)                                                                                                                gCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCa                                                                     >  1:537305/1‑112 (MQ=255)                                                                                                                gCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCa                                                                     <  2:537305/112‑1 (MQ=255)                                                                                                                           gTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATg                    <  1:125382/150‑1 (MQ=255)                                                                                                                                       tGGAACATCTCGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGa                                               <  2:448519/113‑1 (MQ=255)                                                                                                                                       tGGAACATCTCGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGa                                               >  1:448519/1‑113 (MQ=255)                                                                                                                                       tGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGcc                                                 >  2:931793/1‑111 (MQ=255)                                                                                                                                       tGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGcc                                                 <  1:931793/111‑1 (MQ=255)                                                                                                                                         gAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATGCAGCTTGGCCaa        >  1:150956/1‑150 (MQ=255)                                                                                                                                             aTCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATGCAGCTTTGCCAATTCg    >  2:332968/1‑150 (MQ=255)                                                                                                                                             aTCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATGCAGCTTGGCCAATTCg    >  1:925823/1‑150 (MQ=255)                                                                                                                                               cGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATGCAGCTTGGCCAATTCGtt  <  1:457747/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    GCCGGGTTTTCGGTCTCGTCCCAGTACGGGTAACCGATCTTGGCCAGCGCTGCCGGCACCAGGTGACGTTCGTCCTCCGGCACCTGCAGCCCCGCCACCACGCGCCCGTCAGCCGCGCCATGGTTGCG‑GTAG‑TGGAACATCGAGATGTTCCAGCGCCCGCCCAGCTTGTTGAGGAAGTTGAACAGTGCCCCTGGCCGCTCGGGGAATTCGAAGCGCAGCACCATTTCGTCGCTGGCACCGGCCGAGTGGCCGCCGACCATATGACGAATATGCAGCTTGGCCAATTCGTT  >  NC_002947/5874734‑5875023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑