Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,539,106	G→A	8.0%	E197K (GAA→AAA)	PP_4027 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,539,106	0	G	A	8.0%	140.3 / 2.9	50	E197K (GAA→AAA)	PP_4027	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/23);  new base A (2/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.56e-01

TTGAGCGTGACATACCAGAAGCAGCACAACTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTCCCCCCAAGCGACAC  >  NC_002947/4538963‑4539250                                                                                                                                                |                                                                                                                                                  ttGAGCGTGACATACCAGAAGCAGCACAACTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAAt                                                                                                                                                >  4:323244/1‑147 (MQ=255)               ccAGAAGCAGCACAACTTCTGTCGCATCACATCCTCCGAAAGCTGGTATAGCGATTACAGTATCTCACCGCTTAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTgg                                                                                                                                 <  4:257591/148‑1 (MQ=255)                     gcagcaCAACTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACaaaa                                                                                                                          >  4:143364/1‑149 (MQ=255)                        gcaCAACTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGATTACAGAACTACAGTCTGGATTGAAACTCAACGAATTAGCAGCTGTTCTGGAACAAAATc                                                                                                                        >  4:228760/1‑148 (MQ=255)                              cTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAg                                                                                                                     <  6:192516/145‑1 (MQ=255)                              cTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAg                                                                                                                     >  5:192516/1‑145 (MQ=255)                                   gTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCTCTGTCAGCAGGCTTACAGAACTACAGTCTTGATTGACACTCCACGAATTAGCCGCTGTTGTGGCAAAAAATCCAGG‑CCTTcca                                                                                                            <  6:277982/148‑1 (MQ=255)                                      gCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACTAAATCCAGG‑CCTACcaccac                                                                                                        >  6:7155/1‑149 (MQ=255)                                      gCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCcaccac                                                                                                        >  1:55134/1‑149 (MQ=255)                                        aTAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTc                                                                                                              <  8:250840/141‑1 (MQ=255)                                        aTAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTc                                                                                                              >  7:250840/1‑141 (MQ=255)                                              tcctccCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTAt                                                                                                >  3:336507/1‑149 (MQ=255)                                              tcctccCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTAt                                                                                                <  6:157768/149‑1 (MQ=255)                                                     aaaGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATc                                                                                                                        <  4:172998/119‑1 (MQ=255)                                                     aaaGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATc                                                                                                                        <  4:178825/119‑1 (MQ=255)                                                     aaaGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGaaa                                                                                         <  4:336507/149‑1 (MQ=255)                                                         cttgTAAAGCGATTACAGTATCTCATCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAg                                                                                     <  2:11003/146‑1 (MQ=255)                                                               aaGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCaga                                                                               <  4:198160/149‑1 (MQ=255)                                                                        cAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCTCAAAATCCAGGCCCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAg                                                                       <  1:259346/149‑1 (MQ=255)                                                                           tATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGtct                                                                   >  6:101700/1‑149 (MQ=255)                                                                             tctcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGtctc                                                                  <  1:134012/148‑1 (MQ=255)                                                                             tctcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTcc                                                                 >  8:20984/1‑149 (MQ=255)                                                                              ctcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTcc                                                                 >  7:20732/1‑148 (MQ=255)                                                                               tcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTa                                                                        <  6:34227/140‑1 (MQ=255)                                                                               tcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTa                                                                        >  5:34227/1‑140 (MQ=255)                                                                               tcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTccc                                                                >  8:142681/1‑148 (MQ=255)                                                                               tcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTccc                                                                >  8:256911/1‑148 (MQ=255)                                                                               tcACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTccc                                                                >  7:55187/1‑148 (MQ=255)                                                                                  ccGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGCATTAGCCGCTGTTCAGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAAc                                                            >  7:241826/1‑149 (MQ=255)                                                                                         gATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTg                                                                                                                                  <  6:197824/73‑1 (MQ=255)                                                                                          aTCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACAAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCtttttt                                                    >  5:275907/1‑149 (MQ=255)                                                                                          aTCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACAAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCtttttt                                                    >  5:270698/1‑149 (MQ=255)                                                                                             gAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCg                                                 <  3:143364/149‑1 (MQ=255)                                                                                             gAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAAATAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCg                                                 <  5:7155/149‑1 (MQ=255)                                                                                              aaGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCgg                                                <  7:256911/149‑1 (MQ=255)                                                                                                  cACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCaa                                            <  7:20984/149‑1 (MQ=255)                                                                                                   aCTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACAAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAAt                                           <  6:275907/149‑1 (MQ=255)                                                                                                   aCTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACAAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAAt                                           <  6:270698/149‑1 (MQ=255)                                                                                                       tCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCTAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGaa                                        <  3:228760/148‑1 (MQ=255)                                                                                                          gcagGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATAc                                     >  7:46940/1‑148 (MQ=255)                                                                                                                ttACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACg                               >  4:80553/1‑148 (MQ=255)                                                                                                                       aCTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGTCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACgcagggcag                       <  2:55134/149‑1 (MQ=255)                                                                                                                        cTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACgcagggcagg                      <  5:101700/149‑1 (MQ=255)                                                                                                                                  gATTGCCACTCAACGAATTTGCCGCTGTTCTGCCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCATCCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTcccc             <  8:241826/148‑1 (MQ=255)                                                                                                                                  gATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTccccc            >  1:69359/1‑149 (MQ=255)                                                                                                                                  gATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTcccc             <  8:55187/148‑1 (MQ=255)                                                                                                                                       acacTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTCCCCCCAAGc       >  1:351176/1‑149 (MQ=255)                                                                                                                                       acacTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGC‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGACCTTAGGTCTCCCCAACCCTTTTTATCGGGCAATGAATACCATACGCAGGGAAGGGAGCTCCCCCCAAGc       >  6:317321/1‑149 (MQ=255)                                                                                                                                             cACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTCCCCCCAAGCGacac  >  6:169386/1‑148 (MQ=255)                                                                                                                                             cACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTCCCCCCAAGCGacac  >  2:146250/1‑148 (MQ=255)                                                                                                                                                |                                                                                                                                                  TTGAGCGTGACATACCAGAAGCAGCACAACTTCTGTCGCATAACATCCTCCCAAAGCTGGTAAAGCGATTACAGTATCTCACCGCTAAGATCGAAGCCACTGTCAGCAGGCTTACAGAACTACAGTCTGGATTGACACTCCACGAATTAGCCGCTGTTCTGGCACAAAATCCAGG‑CCTTCCACCACCGCCGTATTCCGAAACTAGCCCAGAGAGCTTAGGTCTCCCCAACCCTTTTTTTCGGGCAATGAATACCATACGCAGGGCAGGGAGCTCCCCCCAAGCGACAC  >  NC_002947/4538963‑4539250

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: ‑