Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,831,780	T→C	12.2%	L220P (CTG→CCG)	yfiP →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,831,780	0	T	C	12.2%	97.4 / 6.0	41	L220P (CTG→CCG)	yfiP	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (16/20);  new base C (2/3);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.65e-01

CTGCGGCGCTCCAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGACGGCAGGGCGATTGGCTTGATCTCC  >  NC_002947/1831632‑1831920                                                                                                                                                         |                                                                                                                                                cTGCGGCGCTCCAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCt                                                                                                                                                 <  3:93576/149‑1 (MQ=255)     ggcgCTCCAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑g                                                                                                                                          >  2:112035/1‑149 (MQ=255)         cTCCAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCtt                                                                                                                                       >  6:211930/1‑148 (MQ=255)         cTCCAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCAGTC‑‑GCC‑GCTTg                                                                                                                                      <  4:38213/149‑1 (MQ=255)            cAAGCGCGATGATCATTTCTGTACGGCCGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCAGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGAc                                                                                                                                    <  5:211930/148‑1 (MQ=255)            cAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACg                                                                                                                                   >  3:61018/1‑149 (MQ=255)             aaGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCAGCC‑‑GCC‑GCTTGCCg                                                                                                                                   >  6:12205/1‑148 (MQ=255)             aaGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCAGCC‑‑GCC‑GCTTGCCg                                                                                                                                   <  5:12205/148‑1 (MQ=255)                 gcgATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGCTCGTCAA‑‑‑‑GCGGCAGCC‑‑GCC‑GCTTGCCgctcag                                                                                                                              <  1:348/149‑6 (MQ=38)                   gatgatCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGga                                                                                                                            <  1:2218/149‑1 (MQ=255)                     tgatCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGgac                                                                                                                           >  1:294584/1‑148 (MQ=255)                                 tACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACccacca                                                                                                                <  4:89828/147‑1 (MQ=255)                                      cAGAAGTTGCGGAGATGTGCCTGGACCTTGCTGGCTATGGCCAGGCTTTGCAGTCGCTGGATGCCTATATGGATGTGTTCAGCTTGCATTACCTGTGATGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GGTTGACGAGCAGGACGACTCGGACCAGCGtttt                                                                                                         <  2:320582/149‑2 (MQ=255)                                          aGTTGCGGCGTCTTCCCTGGACCTTGCTGTCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCAt                                                                                                      <  1:304552/148‑1 (MQ=255)                                             tGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATAcc                                                                                                   <  2:294584/148‑1 (MQ=255)                                              gcggcgATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCtt                                                                                                 >  5:135843/1‑149 (MQ=255)                                               cggcgATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTc                                                                                                <  7:160980/149‑1 (MQ=255)                                                            ggACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCt                                                                                                  <  2:127430/134‑1 (MQ=255)                                                            ggACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCt                                                                                                  >  1:127430/1‑134 (MQ=255)                                                             gACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAggg                                                                                  >  7:39012/1‑149 (MQ=255)                                                             gACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAgg                                                                                   <  5:90103/148‑1 (MQ=255)                                                                gttGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCGTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GTC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGc                                                                                <  3:74692/147‑1 (MQ=255)                                                                         gATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGCCGACACCCACCCGCGGTTGCATACCATCCAAGAGTCCAAGGGCCACAACCCCtc                                                                      >  8:90018/1‑148 (MQ=255)                                                                                aGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGt                                                               >  4:180832/1‑149 (MQ=255)                                                                                aGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGt                                                               <  6:12842/149‑1 (MQ=255)                                                                                      cGCAGGCGCTGGATGACTATCTGGATGTGTTCAGCCTGCATTACATGAGCGGCAACCCTCCGGCGGCTCCTCCAGCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCttt                                                                  <  1:112035/147‑1 (MQ=255)                                                                                           gcgcTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCt                                                                                              <  5:269765/107‑1 (MQ=255)                                                                                           gcgcTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCt                                                                                              >  6:269765/1‑107 (MQ=255)                                                                                                    gCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTgg                                             >  2:237939/1‑147 (MQ=255)                                                                                                             gATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAg                                      <  8:39012/145‑1 (MQ=255)                                                                                                             gATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTg                                  <  3:180832/149‑1 (MQ=255)                                                                                                                gtgtTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGc                               >  4:118785/1‑149 (MQ=255)                                                                                                                 tgtTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCCGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGc                               <  7:90018/148‑1 (MQ=255)                                                                                                                 tgtTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGGGGGc                               <  5:197258/148‑1 (MQ=255)                                                                                                                      aGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGAc                          <  4:61018/148‑1 (MQ=255)                                                                                                                       gCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGACgg                        >  1:118148/1‑149 (MQ=255)                                                                                                                        ccTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAgggg                                                                                 <  7:95715/91‑1 (MQ=255)                                                                                                                        ccTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAgggg                                                                                 >  8:95715/1‑91 (MQ=255)                                                                                                                                 ccTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGACGGCAGGGCGAtt              >  1:93262/1‑149 (MQ=255)                                                                                                                                     aGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGACGGCAGGGCGATTgg            <  2:49381/147‑1 (MQ=255)                                                                                                                                      tcgtcAA‑‑‑‑GCGGCAGCC‑‑GCC‑GCTTGCCGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGACGGCAGGGCGATTGGGtt         >  7:331055/5‑149 (MQ=255)                                                                                                                                                 gcggcgGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACAAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGATACGGCAGGGCGATTGGCTTGATATcc  >  3:316089/1‑149 (MQ=255)                                                                                                                                                         |                                                                                                                                                CTGCGGCGCTCCAAGCGCGATGATCATTTCTGTACGGCAGAAGTTGCGGCGATGTGCCTGGACCTTGCTGGCGATGGCCAGGCTTCGCAGGCGCTGGATGCCTATCTGGATGTGTTCAGCCTGCATTACCTGAGCGGCAA‑‑‑‑GCGGCGGCT‑‑GCC‑GCTTGACGAGCAGGACGACACCCACCAGCGTTTGCATACCTTCCTATAGTCCAAGGGGCACAACCCCTGCTTTGGTTCATAATGACGGAGCTGGCAGCCAGGGTGGGCGAGACGGCAGGGCGATTGGCTTGATCTCC  >  NC_002947/1831632‑1831920

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: ‑