Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,610,150	C→T	8.3%	L213L (CTG→TTG)	PP_4081 →	type IV/VI secretion system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,610,150	0	C	T	8.3%	132.3 / 2.2	48	L213L (CTG→TTG)	PP_4081	type IV/VI secretion system protein
Reads supporting (aligned to +/- strand):  ref base C (24/20);  new base T (2/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-01

AAAAATCTTCACCGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGC  >  NC_002947/4610008‑4610292                                                                                                                                               |                                                                                                                                                aaaaaTCTTCACCGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGAtt                                                                                                                                            >  1:181546/1‑148 (MQ=34)  aaaaTCTTCACCGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCa                                                                                                                                          >  3:101255/1‑149 (MQ=34)          cACCGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCaa                                                                                                                                      <  2:203716/145‑1 (MQ=34)           aCCGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCa                                                                                                                                 >  7:55153/1‑149 (MQ=34)            ccGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACGGGAGTTAATGTACTTAGCCCTGTGCCGTGGGCTGAAGGGCAAGTATTCGCTCGCGCCGAAAGGCGAAGCAACACTAAACGCACTGATTAACCAAATGCAc                                                                                                                                >  1:82645/1‑149 (MQ=11)             cGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACt                                                                                                                                    <  6:62592/144‑1 (MQ=34)             cGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACt                                                                                                                                    >  5:62592/1‑144 (MQ=34)                 aTTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGa                                                                                                                            <  4:154328/148‑1 (MQ=34)                                cAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTgc                                                                                                             <  6:253524/148‑1 (MQ=34)                                 aGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTgcgc                                                                                                           >  5:150388/1‑149 (MQ=34)                                                 tCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCgaa                                                                                            <  6:238608/148‑1 (MQ=37)                                                  cAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAc                                                                                                   <  7:288199/140‑1 (MQ=37)                                                  cAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAc                                                                                                   >  8:288199/1‑140 (MQ=37)                                                     gACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAccccc                                                                                               <  6:42783/141‑1 (MQ=37)                                                     gACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCAccccc                                                                                               >  5:42783/1‑141 (MQ=37)                                                      aCGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTc                                                                                      <  4:101255/149‑1 (MQ=37)                                                             ggAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGAcc                                                                               >  6:220116/1‑149 (MQ=37)                                                              gAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCcgcg                                                                                                                   >  7:109595/1‑112 (MQ=35)                                                              gAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCcgcg                                                                                                                   <  8:109595/112‑1 (MQ=35)                                                              gAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGAccc                                                                              <  2:181546/149‑1 (MQ=37)                                                                gagcgcgtacttgcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGAcccc                                                                             >  5:113793‑M2/44‑148 (MQ=255)                                                                    gcgtacttgcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGAcc                                                                               >  4:127155‑M2/40‑142 (MQ=255)                                                                    gcgtacttgcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGAcc                                                                               <  3:127155‑M2/103‑1 (MQ=255)                                                                            gcccttcagcccaaggcacagggcgaagtacGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCATTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCTACCCCCGAAGAAGTCTGCGACCCC‑TACACCAATGt                                                                 <  6:113793‑M2/116‑1 (MQ=255)                                                                                   tgCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCa                                                         <  2:82645/148‑1 (MQ=255)                                                                                         gggCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGCAGTATGCGCCCCA‑TACACCAACGTCGCCCCCAGAAACtt                                                  >  2:96354/1‑149 (MQ=255)                                                                                           gCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCTAAGAAGTCTGCTACCCC‑TACACCAACGTCGCCCCCAGAAACTTcc                                                <  6:150388/149‑1 (MQ=255)                                                                                           gCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTcc                                                <  8:55153/149‑1 (MQ=255)                                                                                                 gggCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACt                                                                                                                                                >  8:109947/1‑48 (MQ=255)                                                                                                 gggCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACt                                                                                                                                                <  7:109947/48‑1 (MQ=255)                                                                                                   gCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGc                                        >  3:237879/1‑149 (MQ=255)                                                                                                          tGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCAt                                            <  6:226065/138‑1 (MQ=255)                                                                                                             gcTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGc                              >  4:199675/1‑149 (MQ=255)                                                                                                                    ccGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgtggtg                       <  4:237879/149‑1 (MQ=255)                                                                                                                     cGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgtggtg                       >  2:271734/1‑148 (MQ=255)                                                                                                                         aGGCGAAGAAACACTCAACGCACTGAATCACCAACTGCACGGGATCATCCGCGAACTGCTCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGc                   <  1:96354/149‑1 (MQ=255)                                                                                                                           gCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGata                                  <  1:211732/131‑1 (MQ=255)                                                                                                                           gCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCg                >  6:16426/1‑149 (MQ=255)                                                                                                                           gCGAAGAAACACTCAACGCACTCATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGata                                  >  2:211732/1‑131 (MQ=255)                                                                                                                             gaagaaACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgt                           >  1:101598/1‑136 (MQ=255)                                                                                                                             gaagaaACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCgt                           <  2:101598/136‑1 (MQ=255)                                                                                                                                   acacTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCAt        <  1:271734/149‑1 (MQ=255)                                                                                                                                       tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGCCCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTcc    >  8:242097/1‑149 (MQ=255)                                                                                                                                       tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCAt                                            >  4:178000/1‑109 (MQ=255)                                                                                                                                       tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTcc    >  8:33918/1‑149 (MQ=255)                                                                                                                                       tCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGGGGTGGAGCCCGTTGGTCATCTcc    >  8:193858/1‑149 (MQ=255)                                                                                                                                         aaCGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCcgc  >  2:319280/1‑149 (MQ=255)                                                                                                                                         aaCGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCcgc  >  2:314184/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                AAAAATCTTCACCGTGATTACCCGCCTGATGCAGGAGCCCAAGCGTTATCAGGACGTACTGGAGTTCATGTACTTCGCCCTGTGCCTTGGGCTGAAGGGCAAGTATGCGCTCGCGCCGAAAGGCGAAGAAACACTCAACGCACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCC‑TACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGC  >  NC_002947/4610008‑4610292

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: ‑