Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,751,079	T→G	20.8%	P146P (CCT→CCG)	PP_1551 →	replication protein O

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,751,079	0	T	G	20.8%	70.1 / 13.6	42	P146P (CCT→CCG)	PP_1551	replication protein O
Reads supporting (aligned to +/- strand):  ref base T (10/23);  new base G (7/2);  total (17/25)
Fisher's exact test for biased strand distribution p-value = 1.91e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

GAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGC  >  NC_002947/1750935‑1751226                                                                                                                                                  |                                                                                                                                                     gAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGACAGAGCCTAAGTAA‑ATcttcctagg                                                                                                                                                   >  6:263798/1‑145 (MQ=255)     gACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGa                                                                                                                                             <  1:5495/149‑1 (MQ=255)      aCTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAC‑ATCTTCCGA‑AGGAAGAt                                                                                                                                            <  1:281977/149‑1 (MQ=255)        tGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTACGT‑CGGAAGATGt                                                                                                                                          >  1:202912/1‑149 (MQ=255)          gATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATCCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGtt                                                                                                                                         <  1:267668/148‑1 (MQ=255)            ggtccGTTGATCCGACACAGACCAAAACAGCCGACTCGGCTGAAGTTGTCCGAATCGTCTCAGAGTCGAACCAGACCAAAACCGCCGACTCCCTTCTTTATTCTCAGAAAGACACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGAT‑TTACAt                                                                                                                                     <  5:294009/145‑1 (MQ=255)                      tCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAGCCCCCCAATGTAA‑ATCTTGCGT‑GGGGAGATGGTACATGCCCCCCCa                                                                                                                            >  8:348167/1‑149 (MQ=255)                       ccGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCGCCTCTGGAA‑ATCTGGCTG‑GGGAAGATGGTTCATGAGACCCCAg                                                                                                                           >  6:134177/1‑149 (MQ=255)                         gAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCg                                                                                                                         <  5:321918/149‑1 (MQ=255)                               gACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCCGGAAGATGTTACATGCCCCCCCAGCgagccg                                                                                                                    <  1:45561/149‑1 (MQ=255)                                  cAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGACACGGCCTAGGTTA‑ATCTTCCTG‑CGTAAGATGTTACATGGCCCGCCAGCgcgccggcgc                                                                                                                >  8:158715/1‑149 (MQ=255)                                  cAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCGATGTAA‑ATCTTACTG‑CGGAAGATGTTACATTCACACCCAGCgagccggcgc                                                                                                                >  2:139830/1‑149 (MQ=255)                                  aaaaaCCGCAGAGTCGGCTTAAGTGTTCAGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAATAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCgagccggagc                                                                                                                <  8:302742/148‑1 (MQ=255)                                            gACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATATTGCTT‑CGGAAGATGGTAGATGACCACCCACCGCGCCCGCGCCGACGCCCGc                                                                                                      >  2:224652/1‑149 (MQ=255)                                                 ggCTGAAGTGGTCCTAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAgg                                                                                                 <  3:216052/149‑1 (MQ=255)                                                 ggCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAg                                                                                                  <  5:263798/148‑1 (MQ=255)                                                   cTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAg                                                                                                  <  1:62498/146‑1 (MQ=255)                                                   cTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGAt                                                                                               <  3:312705/149‑1 (MQ=255)                                                      atttgttCCGAATCGGATCAGAGTCTAAACATACAAAAACTGCAGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCACCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGa                                                                                             <  8:337732/142‑1 (MQ=255)                                                      aaGTGGTCCGAATCGGCTATGAGTAGAAACAGTCCAAAAACGCCGACTCCCTTCTTTATTCTAATAAAGAAACCCCCAATGTAA‑ATATTCCTT‑CGGAATATGTTACATGCCCACCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGa                                                                                             <  6:35453/148‑1 (MQ=255)                                                                         agagTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCAAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCgg                                                                           <  7:348167/147‑1 (MQ=255)                                                                         agagTCGAAACACACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCgg                                                                           <  4:262994/147‑1 (MQ=255)                                                                           agTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCaaa                                                                       <  5:296310/149‑1 (MQ=255)                                                                            gTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCaaa                                                                       <  5:134177/148‑1 (MQ=255)                                                                                  aCAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCa                                                                <  6:187210/149‑1 (MQ=255)                                                                                       ccAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAGCGCCCGATGTAA‑ATCTTGGTT‑GGGGAGATGTTACATGAGGCCCAAGCGAGGCGGGGCCGCGACCGGCGAAGGAGGAGCGCAAGGCGACCAACGGGAAAgccgcacagcgg                                                           >  4:177597/1‑142 (MQ=255)                                                                                        cAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAGGCGCCCGATGTAA‑ATCTTACTT‑CGGCAGATGTTAGATGCACCCCCAGCGACCCGGAGCCGACGCCGGCCAAGCAGGCGCGCAAGGCGCACTGCGCCCAAGCCGCCAAGCTgg                                                          >  4:203708/1‑149 (MQ=255)                                                                                                 cgACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATc                                                 <  7:158715/149‑1 (MQ=255)                                                                                                       ccTTCTTTATTCTAAGAAAGAGGCGCCCTATGTAA‑ATCTTCATT‑CGGAAGAGGTTACATGACCCCCCGGCGACCCGCCGCCGACACCGGCCCAGGAGGAGCGGCAGGCGCCCATCGGCAAAGCCGCCAGGCTGGCCCGCAAGCCGCCCg                                           >  2:124402/1‑149 (MQ=255)                                                                                                       ccTTCTTTATTCTAAGAAAGAACCCCCCTATGTAA‑ATCTTGCTT‑AGGAAGATGTTACAAGCCAACACAGCGAGCCGGAGCCGACTACGGCCAAGGGAGACCGAAAGGCACCCTACGGCAAACACCCCATGCAGGCCGACAAACCGCAcc                                           >  6:381288/1‑148 (MQ=255)                                                                                                       ccTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGAt                                                                                                                                            <  4:362277/52‑1 (MQ=255)                                                                                                       ccTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGAt                                                                                                                                            >  3:362277/1‑52 (MQ=255)                                                                                                                   tAAGAAAGAAGCCCCCTATGTAA‑ATCTTCCGT‑GGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGGAAGGCGCCCTTCGGCGAAGCCGCCACGCAGGCCGACCATCCGCACGGGCGCGaggcat                               >  8:285810/1‑144 (MQ=255)                                                                                                                             aCCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGc                     <  3:177597/149‑1 (MQ=255)                                                                                                                                 ccTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGAt                 >  5:211033/1‑149 (MQ=255)                                                                                                                                    aTGTAACATCTTCCGA‑AGGAAGAT‑TTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTAc              >  5:124671/1‑149 (MQ=255)                                                                                                                                     tgtaacaTCTTCCGA‑AGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTg                   >  8:286275/7‑144 (MQ=255)                                                                                                                                     tgtaacaTCTTCCGA‑AGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTg                   <  7:286275/138‑1 (MQ=255)                                                                                                                                      gtaacaTCTTCCGA‑AGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACt             >  5:195193/6‑149 (MQ=255)                                                                                                                                         a‑aTCTTCGTT‑CGGTAGATGTTACTTGGCCCCCCAGGGAGCGGGAGGCGAGTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGGAAAGCGGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  5:307229/148‑1 (MQ=255)                                                                                                                                         a‑aTCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  2:202912/148‑1 (MQ=255)                                                                                                                                          caTCTTCCGA‑AGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGc         >  8:351939/2‑149 (MQ=255)                                                                                                                                           aTCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCt        <  6:211033/149‑1 (MQ=255)                                                                                                                                                cctt‑cGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGCCTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCGGATCGCTGATTACTTGGCTGTCCg   >  3:42284/1‑149 (MQ=255)                                                                                                                                                cctt‑cGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGa                  <  1:162726/134‑1 (MQ=255)                                                                                                                                                cctt‑cGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGa                  >  2:162726/1‑134 (MQ=255)                                                                                                                                                cctt‑cGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCg   >  3:46499/1‑149 (MQ=255)                                                                                                                                                  tt‑cGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGc  >  8:208918/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                                     GAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTT‑CGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGC  >  NC_002947/1750935‑1751226

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: ‑