Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,967,636	T→C	8.3%	D14G (GAT→GGT)	fliD ←	flagellar filament capping protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,967,636	0	T	C	8.3%	132.2 / 2.8	48	D14G (GAT→GGT)	fliD	flagellar filament capping protein
Reads supporting (aligned to +/- strand):  ref base T (23/21);  new base C (2/2);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

AATCGCAGAGCGGAAGGTATCCAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTACACATTGTCATCAAGTAAAAAA  >  NC_002947/4967491‑4967784                                                                                                                                                  |                                                                                                                                                     aaTCGCAGAGCGGAAGGTATCCAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGa                                                                                                                                                   >  8:45492/1‑149 (MQ=255) aaTCGCAGAGCGGAAGGTATCCAATGCATTCTTAATCATGCCCACAGCAGACACTATTCTGGTCGTAGTCTTCTGTTGACTAGTGATCTGCTGATGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCCACTGGGTATCGa                                                                                                                                                   >  5:369249/1‑149 (MQ=255)  aTCGCAGAGCGGAAGGTATCAAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGAc                                                                                                                                                  >  6:367447/1‑149 (MQ=255)                  tATCCAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCa                                                                                                                                  >  6:113718/1‑149 (MQ=255)                    tCCAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGGCTCTGGCGTCGATAccca                                                                                                                                 <  1:142023/148‑3 (MQ=255)                    tCCAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCac                                                                                                                                 <  5:113718/148‑1 (MQ=255)                       aaTGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCactgac                                                                                                                             >  5:91964/1‑149 (MQ=255)                       aaTGCATTCTTAATCAGGCCCACCGCAGACACTTGGGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCactgac                                                                                                                             <  8:239551/149‑1 (MQ=255)                           ctttcttcATCATGGCCCCCGCAGACACTTGTGTGGTCGTTGTCTTCTGTTGAGTAGTGATGTGCTGATGCTTGGGCGCCTTTTGGGCATCGTCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACtgtt                                                                                                                         <  6:369249/147‑1 (MQ=255)                               cTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTa                                                                                                                      <  7:76842/148‑1 (MQ=255)                                           cacaGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCtt                                                                                                         <  3:280985/149‑1 (MQ=255)                                           cacaGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCtt                                                                                                         >  4:280985/1‑149 (MQ=255)                                                               tCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTTGGCGCCTTTTCGGCATCTTCCAGAGCCTTGACAATCGACTTGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTTATCAGCGAAt                                                                                     <  5:263702/149‑1 (MQ=255)                                                               tCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCact                                                                                                                                >  2:317327/1‑106 (MQ=255)                                                               tCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCact                                                                                                                                <  1:317327/106‑1 (MQ=255)                                                               tCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAAt                                                                                     >  3:61627/1‑149 (MQ=255)                                                                       ttctGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAAtt                                                                              >  4:137704/1‑148 (MQ=255)                                                                         ctGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCATTTCGTCATCGGCCAGAGCCTTGACAATCGACTGGGTATAGACGACGGAGACGATAACACTGACTGTTGTAATTTCCATTGCTTTATATCCATGATCAGCGAATGCCAAATGCt                                                                           >  2:304363/1‑149 (MQ=255)                                                                               agtagtGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGa                                                                     >  3:354821/1‑149 (MQ=255)                                                                                    tGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGatgaat                                                                <  4:354821/149‑1 (MQ=255)                                                                                        ctgctgTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGc                                                            >  5:259635/1‑149 (MQ=255)                                                                                         tgctgTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACg                                                                      <  7:341643/138‑1 (MQ=255)                                                                                         tgctgTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACg                                                                      >  8:341643/1‑138 (MQ=255)                                                                                              ttGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        <  7:45492/147‑1 (MQ=255)                                                                                              ttGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGaca                                                      >  5:299451/1‑149 (MQ=255)                                                                                                    gggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATc                                                 <  5:341915/148‑1 (MQ=255)                                                                                                    gggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTCTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        <  1:357666/141‑1 (MQ=255)                                                                                                    gggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTCTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        >  2:357666/1‑141 (MQ=255)                                                                                                     ggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTACCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        <  5:65374/140‑1 (MQ=255)                                                                                                     ggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTACCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        <  5:70620/140‑1 (MQ=255)                                                                                                     ggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTACCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        >  6:70620/1‑140 (MQ=255)                                                                                                     ggCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTACCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCgaga                                                        >  6:65374/1‑140 (MQ=255)                                                                                                      gcgcCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGa                                              <  3:137704/149‑1 (MQ=255)                                                                                                                 gCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATAGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCa                                   >  5:275092/1‑149 (MQ=255)                                                                                                                  cATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCAATGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCAt                                  <  5:367447/149‑1 (MQ=255)                                                                                                                      ggCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACg                                                                      >  2:320562/1‑109 (MQ=255)                                                                                                                      ggCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACg                                                                      <  1:320562/109‑1 (MQ=255)                                                                                                                             gCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTa                        <  1:304363/148‑1 (MQ=255)                                                                                                                                ttGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTAcaca                    >  6:200120/1‑149 (MQ=255)                                                                                                                                    cAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGatgaatga                                                              >  7:309075/1‑103 (MQ=255)                                                                                                                                    cAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGatgaatga                                                              <  8:309075/103‑1 (MQ=255)                                                                                                                                            gtggTATCGGCTCCGGCGTCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTACACATTGTCATCAAg         >  5:198829/3‑148 (MQ=255)                                                                                                                                              ggTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCAt                                  <  6:213518/121‑1 (MQ=255)                                                                                                                                              ggTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCAt                                  >  5:213518/1‑121 (MQ=255)                                                                                                                                              ggTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACa                           <  2:264408/128‑1 (MQ=255)                                                                                                                                              ggTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACa                           >  1:264408/1‑128 (MQ=255)                                                                                                                                              ggTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTACACATTGTCATCAAGt        <  6:259635/147‑1 (MQ=255)                                                                                                                                                tATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTACACATTGTCATCAAGTaaa     >  8:25829/1‑148 (MQ=255)                                                                                                                                                  tCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTACACATTGTCATCAAGTaaaaaa  <  7:25829/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     AATCGCAGAGCGGAAGGTATCCAATGCATTCTTAATCATGCCCACAGCAGACACTTGTGTGGTCGTAGTCTTCTGTTGAGTAGTGATCTGCTGTTGCTTGGGCGCCTTTTCGGCATCGGCCAGAGCCTTGACAATCGACTGGGTATCGACGCCGGAGCCGATACCACTGACTGTTGTACTTGCCATTGCTTTATATCCCTGATCAGCGAATGCCAATTGCTTGACGATGAATGAGCGAGACACAATCCGAGTCAAGACTCATGCCAACATTACACATTGTCATCAAGTAAAAAA  >  NC_002947/4967491‑4967784

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: ‑