Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,148	G→A	8.9%	intergenic (‑112/‑156)	PP_5175 ← / → PP_5176	HlyD family secretion protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,903,148	0	G	A	8.9%	123.7 / 2.1	45	intergenic (‑112/‑156)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (15/26);  new base A (2/2);  total (17/28)
Fisher's exact test for biased strand distribution p-value = 6.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.50e-01

CCAGGCAGACAACCGACAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAG  >  NC_002947/5903000‑5903279                                                                                                                                                      |                                                                                                                                     ccAGGCAGACAACCGACAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCggg                                                                                                                                      >  1:333101/1‑149 (MQ=255)   aGGCAGACAACCGACAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCggggg                                                                                                                                    >  5:331913/1‑149 (MQ=255)             ccGACAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTagcg                                                                                                                          >  7:256469/1‑149 (MQ=255)                aCAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCGCTTCGCGGGc                                                                                                                       <  2:278825/149‑1 (MQ=255)                aCAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGGAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGc                                                                                                                       <  7:199735/149‑1 (MQ=255)                    cGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGc                                                                                                                   <  2:333101/149‑1 (MQ=255)                     ggtcGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCATGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGcc                                                                                                                  <  5:23607/146‑1 (MQ=255)                         gCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGTGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCcgcg                                                                                                              <  4:176333/149‑1 (MQ=255)                           atcatcGCCTTGCGGTCTCCTTGCTTGTGCTCAAATGATTTGTGGTATGCGACTGTGATGGTAGTTCAGGGTTCGATAAACATCTCTGACGGGGGCCATGCTGGCATTTTTGGAG‑CCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGaa                                                                                                            <  4:55812/149‑1 (MQ=255)                           aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGc                                                                                                                                   >  2:194340/1‑126 (MQ=255)                           aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGc                                                                                                                                   <  1:194340/126‑1 (MQ=255)                           aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGc                                                                                                                                   <  5:324296/126‑1 (MQ=255)                           aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGc                                                                                                                                   >  6:324296/1‑126 (MQ=255)                           aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGAGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCCAATATCGGGCCAGCCcgcgc                                                                                                             >  2:155588/1‑147 (MQ=255)                            tCAACCCCATGCTGGCGCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGTGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAag                                                                                                           <  7:244078/149‑1 (MQ=255)                              aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAagag                                                                                                         <  2:83955/149‑1 (MQ=255)                                cGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTAGCGGGCGCGCCCGCGAAGAGGc                                                                                                       >  3:65142/1‑149 (MQ=255)                                 gCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCAAATAGCGGGCGACCCCGCGAAGAGGc                                                                                                       >  3:167175/1‑148 (MQ=255)                                   cATGCTGGCTCCTTGTTTGTGCAAAATTGATTTGGGGCATGGGACTGTCTGCGTAGTTAAGGGTTCGAAAAACATCACTGACGGGGGCCTTGCTGGCATTTTTGGGG‑CCTGGGGGGGCATCTTGGGGGGCGTGCCCGGGATGAGGCCTc                                                                                                    <  2:209175/149‑1 (MQ=255)                                       cTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCca                                                                                                  >  5:169690/1‑147 (MQ=255)                                              cttgcttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTAGCGGGCGCGCCCGCGAAGAGGGCGCCACAGCCATGt                                                                                         >  4:354977/1‑149 (MQ=255)                                                 gtttgTGCACAAATTTTTTGTGGGATGCGACTGTGAGCGTAGTTCAGTTTTCGTTAAACATCACTGCGGGGGGCCTTGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTGCGCGGGCGAGCCCGCTAAGAGGCCTCCACAGCCATGTAt                                                                                       <  8:256469/146‑1 (MQ=255)                                                            aaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGa                                                                                                             >  4:134558/1‑115 (MQ=255)                                                            aaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGa                                                                                                             <  3:134558/115‑1 (MQ=255)                                                                aTTTGGGGGAGGCGCCTGTGATCGTAGTTCAGGGTTCGATAAACATCTCTGACGGGGGCCTTGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCTCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATc                                                                       <  3:337262/149‑1 (MQ=255)                                                                 tttGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATc                                                                       <  8:353570/148‑1 (MQ=255)                                                                     tgGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCATCACGGGCGGGCCCGCCACAAGGCCGGCACCACCAAGTTTAAGTATATGGCaaataccga                                                                   >  4:173503/1‑143 (MQ=255)                                                                       gtattctaCTGTGAGCGTAGTTCAGGGTTCTATAAACATCACTGACGGGGGCCATGCTGGAATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCGGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAAc                                                                <  4:65142/142‑1 (MQ=255)                                                                       ggATGCGACTGTCCGGTTATTCCCGGGTTCCAAAACCATCACTG‑CGGGGGCCCTGGCGGCAATTTTGGGGCCCTGCGGGGCCCTCTCCGCGGGCGCCCCCGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGaaa                                                                 <  6:35702/148‑1 (MQ=255)                                                                                tgtgAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAagag                                                                                                         >  5:383475/1‑99 (MQ=255)                                                                                tgtgAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAagag                                                                                                         <  6:383475/99‑1 (MQ=255)                                                                                tgtgAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTCTGGTG‑CCTGTGGAGGCCTCTTcg                                                                                                                            >  8:156760/1‑80 (MQ=255)                                                                                tgtgAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTCTGGTG‑CCTGTGGAGGCCTCTTcg                                                                                                                            <  7:156760/80‑1 (MQ=255)                                                                                      cGTAGTTCAGGGTTCGATAAACTTCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGcc                                                 <  3:354977/149‑1 (MQ=255)                                                                                      cGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAg                                                                    >  3:288985/1‑130 (MQ=255)                                                                                      cGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAg                                                                    <  4:288985/130‑1 (MQ=255)                                                                                                              cACTGACGGGGGCCATGCTGGATTTTTTGGTG‑CCTGGGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCttt                        <  4:167175/149‑1 (MQ=255)                                                                                                                cTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCTTTca                      <  6:331913/149‑1 (MQ=255)                                                                                                                 tGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAAc                                  <  7:99697/136‑1 (MQ=255)                                                                                                                   ccGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGTGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCTTTcaca                    <  8:325482/147‑1 (MQ=255)                                                                                                                        ggCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCTTTCACAGGGAgg              <  6:169690/149‑1 (MQ=255)                                                                                                                                tGGCATTTTTGGTG‑CCTGCGGGGGCCTATTAGCGGGCGAGCCCGCGAAGAGGGCTACACAGCCAAGTATCAGTATATGCCATATGCAGAAACCATCAGGCCTCGGCCAT‑CCCCGTTGCCACCGCGACCATTCACACGGAGGCGCACAt       >  2:280560/1‑148 (MQ=255)                                                                                                                                 ggCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGGAGCGGCCGCGACAGCCATGTATCAGTATCTGCCAGATCCCGGAACCATCAGGCCTCGGCCAT‑CCCCGTTCCCACCGCTACCGTTGACCGGGAGGCTcacagt      >  8:269017/1‑146 (MQ=255)                                                                                                                                   cATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa   <  5:129320/149‑1 (MQ=255)                                                                                                                                    aTTTTTGGTG‑CCTGCGGGGGCCGAATAGCGGGCGGGCCCCCGAAGAGGGCGCCCCACCCAAGTTTAAATATATGGCAAATACAGAAAACCACAGGCATAGGCCCTACCCCGTACC‑ACCCCGAACGTTGACAAGGGGGCGCACATTGAAg  >  4:17897/1‑149 (MQ=255)                                                                                                                                               gcTGTGGAGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAg                                                          <  7:345739/83‑1 (MQ=255)                                                                                                                                               gcTGTGGAGGCCTCTTAGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGGCATATACAGAAAACATCAg                                                          >  8:345739/2‑84 (MQ=37)                                                                                                                                                      |                                                                                                                                     CCAGGCAGACAACCGACAGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTG‑CCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAT‑CCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAG  >  NC_002947/5903000‑5903279

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑