Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,897,773	G→A	12.7%	intergenic (‑173/+61)	PP_5172 ← / ← PP_5173	hypothetical protein/RND family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,897,773	0	G	A	12.7%	97.9 / 4.2	39	intergenic (‑173/+61)	PP_5172/PP_5173	hypothetical protein/RND family transporter
Reads supporting (aligned to +/- strand):  ref base G (17/17);  new base A (2/3);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.76e-01

CCGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGCCACGAT  >  NC_002947/5897626‑5897920                                                                                                                                                    |                                                                                                                                                     ccGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACggt                                                                                                                                                     <  8:212577/149‑1 (MQ=255)         agGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCgatggtgcatc                                                                                                                                             <  5:102522/149‑6 (MQ=255)         agGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATg                                                                                                                                             <  4:346442/149‑1 (MQ=255)          ggTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGATCGGGTTTACCCGCGAATACGGTGGTCGATg                                                                                                                                             <  4:134608/148‑1 (MQ=255)                aaGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATc                                                                                                                                      >  4:329165/1‑149 (MQ=255)                aaGGGGTTTTGAGCCTCGCTTGAGGGCAATAGTAGTGAGGCTGGATTATTCTTAAAAATACTGTATAAGAATTTTTATATAACCATTTAAGAGAAAACGCCTCTCGTAGGAGCGGGTTTACACGCGAATACTGTGGTAGATGCACCATc                                                                                                                                      >  4:114830/1‑149 (MQ=255)                          gcgcCTGGCTTTAGGGAAATATTAGTTAGGCGGTATTATTATAAAAAATACTGTTAAATAATTTTTATAAAACAATTTAAGACAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTcgcg                                                                                                                             <  1:185280/148‑1 (MQ=37)                           cgcTTGGCTTGTGGGCAATATTCGGGAGGCGGGCTTTTGTTTAAAAATAATTTTTAAGAATTTTTATATTACCATTTACGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCgg                                                                                                                            <  5:253498/148‑1 (MQ=37)                           cgcCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTAAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATTCGCgg                                                                                                                            <  7:314495/148‑1 (MQ=25)                                   ttGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCCCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATTCGCGGGTAAA‑c                                                                                                                     <  5:315054/146‑1 (MQ=21)                                   ttGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCCCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATTCGCGGGTAAA‑c                                                                                                                     >  6:315054/1‑146 (MQ=21)                                     gAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGc                                                                                                                 <  3:114830/148‑1 (MQ=255)                                       gggCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCa                                                                                                                                   <  2:196085/129‑1 (MQ=255)                                       gggCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCa                                                                                                                                   >  1:196085/1‑129 (MQ=255)                                         gCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTAACCGCGAATAAGGTGGTCGATTAACCATAGCATTAGCCGGTAAA‑ACCgataaa                                                                                                             >  7:52105/1‑143 (MQ=255)                                           aaTAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATTCGCgg                                                                                                                            >  1:89371/1‑132 (MQ=25)                                           aaTAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATGCGATGGTGCATCGACCACCGTATTCGCgg                                                                                                                            <  2:89371/132‑1 (MQ=25)                                           aaTAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTAc                                                                                                           >  5:125001/1‑148 (MQ=255)                                                        cGGTATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGTTAAA‑CCCGCTCCTACCAGGGGCCATATgg                                                                                             <  1:220615/149‑1 (MQ=255)                                                          ggATTATTCTTAAAAATACTGTTTAAGAATTTTAATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGGCGATGCACCATCGCATTCGCGGGTAAACCCCGCTCCTACCAGGGGCCATATggg                                                                                            <  1:3793/149‑1 (MQ=255)                                                                ttCTTACAAATCCTGTTTAAGAAGTGTTATCTAACGATTTACTATACCCCGCCTCTGGTCGGAGCGGGTTTACCCGCGAATAGGGTGGGCGCGGCCCCCTCGCATGCGCGGGTAAA‑CCCGCGCCTACCAGGGGCCATAGGGGCCTTCAg                                                                                     <  6:376251/149‑1 (MQ=255)                                                                ttCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTAACCGCGAATACGGTGGTGGATGGACCATCGCATTAGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGGCTTGAg                                                                                     >  3:180696/1‑149 (MQ=37)                                                                                  aaGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCAGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTcg                                                                   >  7:98626/1‑149 (MQ=255)                                                                                           tatataACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACggtg                                                                                                                                                    >  1:312864/1‑60 (MQ=255)                                                                                           tatataACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACggtg                                                                                                                                                    <  2:312864/60‑1 (MQ=255)                                                                                            ataaaACAATTTATCACACCAGGCCTCTGTTTGGTGGTGGTTAACCCCCTATTAGGGTGGTCTATTCACCATCGCATTCGCGGTTAAC‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTg                                                          <  4:180696/148‑1 (MQ=255)                                                                                              ataACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCTTTCGCGGGTAAA‑c                                                                                                                     <  4:208734/87‑1 (MQ=255)                                                                                              ataACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑c                                                                                                                     >  3:208734/1‑87 (MQ=255)                                                                                                aaCCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑c                                                                                                                     >  3:341588/1‑85 (MQ=255)                                                                                                aaCCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑c                                                                                                                     <  4:341588/85‑1 (MQ=255)                                                                                                aaCCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTAc                                                       >  5:290320/1‑147 (MQ=255)                                                                                                aaCCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTAc                                                       >  1:258268/1‑147 (MQ=255)                                                                                                     tttAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCa                                                <  2:258268/149‑1 (MQ=255)                                                                                                        aaGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGGATACGGTGGTCGATGGACCATCGCATTCGCGGGTTAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGGGGTTGTGGGGCTCGCGGAtgttgt                                                         >  5:33150/1‑137 (MQ=25)                                                                                                                    ctctGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCgg                                   >  5:360553/1‑147 (MQ=255)                                                                                                                       tGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAg                                <  6:125001/147‑1 (MQ=255)                                                                                                                       tGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAg                                <  6:290320/147‑1 (MQ=255)                                                                                                                            ggAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAAcagc                         <  3:329165/149‑1 (MQ=255)                                                                                                                                         ccGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAg                                <  4:176952/129‑1 (MQ=255)                                                                                                                                         ccGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAg                                >  3:176952/1‑129 (MQ=255)                                                                                                                                          cgcgAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGt           >  1:129756/1‑149 (MQ=255)                                                                                                                                           gcgAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTc          >  1:334974/1‑149 (MQ=255)                                                                                                                                             gAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGc        >  1:302211/1‑149 (MQ=255)                                                                                                                                                    gtggtCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGCCACgat  >  4:41319/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CCGGGCAGAGGTTTGAAGGGGTTTTGCGCCTGGCTTGAGGGCAATAGTAGTGAGGCGGGATTATTCTTAAAAATACTGTTTAAGAATTTTTATATAACCATTTAAGAGAACACGCCTCTGGTAGGAGCGGGTTTACCCGCGAATACGGTGGTCGATGCACCATCGCATTCGCGGGTAAA‑CCCGCTCCTACCAGGGGCCATATGGGCCTTCAGGCGTGTTTCTGCGGCTCGCGGATCTTGTACCAGGCCACGTACAGCGCCGGCAGGAACAGCAGCGTCAGCAAGGTCGCCACGAT  >  NC_002947/5897626‑5897920

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑