Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,957,895	A→G	100%	S269P (TCG→CCG)	fliG ←	flagellar motor switch protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,957,895	0	A	G	100.0%	165.6 / ‑6.8	50	S269P (TCG→CCG)	fliG	flagellar motor switch protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (25/24);  minor base C (1/0);  total (26/24)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTCTTTCTGCGCGGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGACACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGTCGATTTCACGGATCGCGTCCAT  >  NC_002947/4957757‑4958036                                                                                                                                            |                                                                                                                                               tttctttcTGCGCGGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCa‑a                                                                                                                                      >  7:51464/1‑148 (MQ=255)  ttctttctGCGCGGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑aca                                                                                                                                    >  3:320365/1‑149 (MQ=255)         tGCGCGGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCg                                                                                                                               >  2:250015/1‑147 (MQ=255)           cgcgGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCggag                                                                                                                            <  4:25561/148‑1 (MQ=255)           cgcgGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCggag                                                                                                                            >  4:291216/1‑148 (MQ=255)           cgcgGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCggag                                                                                                                            <  6:247234/148‑1 (MQ=255)              ggTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGaca                                                                                                                        <  6:103333/149‑1 (MQ=255)                    aaCGTCGCTGACACGTACAGCACCTTTGGCCTCCAGATCGTCAAGCAGAAGATCAGAATAACCTTTCGAAAACTTCTTGAAGAAATTGTCCATGACCCGCTCGTC‑GGCGCCCTTCAGCGCCACCACAA‑ACACGAACGAGCACACTTcgc                                                                                                                  >  8:91699/2‑149 (MQ=255)                     aCGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTcgcg                                                                                                                 >  1:70959/1‑149 (MQ=255)                                ccGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGcaccac                                                                                                                                          >  2:315988/1‑114 (MQ=255)                                ccGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGcaccac                                                                                                                                          <  1:315988/114‑1 (MQ=255)                                ccGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTcgc                                                                                                                  >  3:139088/1‑137 (MQ=255)                                ccGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTcgc                                                                                                                  <  4:139088/137‑1 (MQ=255)                                      cGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCACACACGTCGGAGGACACTTCGCGCAAc                                                                                                             <  1:4635/137‑1 (MQ=255)                                      cGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAAc                                                                                                             >  2:4635/1‑136 (MQ=255)                                        gCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGccc                                                                                              <  3:291216/149‑1 (MQ=255)                                        gCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGccc                                                                                              <  5:31165/149‑1 (MQ=255)                                                   tCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGt                                                                                                                                 <  7:181171/103‑1 (MQ=255)                                                   tCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGt                                                                                                                                 >  8:181171/1‑103 (MQ=255)                                                     cAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGAc                                                                                   <  5:312508/147‑1 (MQ=255)                                                                gcagcaGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGgttg                                                                      >  8:247845/1‑149 (MQ=255)                                                                 cagcagTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGGGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGgtc                                                                                         <  8:203662/129‑1 (MQ=255)                                                                 cagcagTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGGGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGgtc                                                                                         >  7:203662/1‑129 (MQ=255)                                                                   gcagTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGttgttg                                                                   <  2:70959/149‑1 (MQ=255)                                                                     agTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGaa                                                                 <  8:42914/149‑1 (MQ=255)                                                                      gTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGttgttg                                                                   >  4:90789/1‑146 (MQ=255)                                                                      gTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAg                                                                <  6:125536/149‑1 (MQ=255)                                                                      gTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGAGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGttgttg                                                                   >  3:132561/1‑146 (MQ=255)                                                                         ccGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGAc                                                              >  6:153898/1‑148 (MQ=255)                                                                           gAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACaaa                                                           <  8:181482/149‑1 (MQ=255)                                                                                       gACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAACCATCAGGTCTTc                                               >  6:59696/1‑149 (MQ=255)                                                                                          aTGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGAt                                            >  8:184954/1‑149 (MQ=255)                                                                                                ttGAAGATCTTGTCCTTGACCCGCTCGTCGGGCGCCCTTGAGCGGCACCACCA‑ACACGt                                                                                                                                 >  1:34611/1‑59 (MQ=255)                                                                                                ttGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGTCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTc                                      >  1:22444/1‑149 (MQ=255)                                                                                                ttGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTc                                      >  8:128458/1‑149 (MQ=255)                                                                                                  gAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTc                                      <  3:90789/147‑1 (MQ=255)                                                                                                        cTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGAt                                            >  2:191187/1‑135 (MQ=255)                                                                                                        cTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGAt                                            <  1:191187/135‑1 (MQ=255)                                                                                                           gTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAg                                <  4:132561/144‑1 (MQ=255)                                                                                                           gTCCTTGACCCGCTCGTC‑GGCGCACTTGAGCGGCACCAACA‑ACACGTCGTAGCACACTTCCCGCAACAGCGCCTGCATGACAAGGTCGTCGACCTCGGCCAAGTTGTTGAAGCCAAACATCAGGTCTTCAATCTGCTCCGCCAGGTCGc                           >  6:183131/1‑149 (MQ=255)                                                                                                            tCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCt                          <  5:153898/149‑1 (MQ=255)                                                                                                             ccTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGAc                                  <  5:318020/140‑1 (MQ=255)                                                                                                             ccTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTAGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCTAc                                  >  6:318020/1‑140 (MQ=255)                                                                                                              cTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAAc                                                          >  5:238466/1‑115 (MQ=255)                                                                                                              cTTGACCCGCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAAc                                                          <  6:238466/115‑1 (MQ=255)                                                                                                              cTTGACCCGCTCGTC‑GGCGCCCTAGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGt                        >  7:204365/1‑149 (MQ=255)                                                                                                                      gCTCGTC‑GGCGCCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGTCGATTTCa                <  8:204365/149‑1 (MQ=255)                                                                                                                               gcgcCCTTGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGTCGATTTCACGGATcgc        <  1:250015/149‑1 (MQ=255)                                                                                                                                  ccgacgAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGTCGATTTCACGGATCGCGTc     <  6:43439/144‑1 (MQ=255)                                                                                                                                     ttGAGCGGCACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGTCGATTTCACGGATCGCGTCCAt  >  7:75549/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                               TTTCTTTCTGCGCGGTTTCCACGTCGCTGACCCGTACCGGCCCTTTGGCCTCCAGATCGTCACGCAGCAGTTCCGAAGCACGTTTGGACATGTTCTTGAAGATCTTGTCCTTGACCCGCTCGTC‑GGCGCCCTTGAGCGACACCACCA‑ACACGTCGGAGGACACTTCGCGCAACAGCGCCTGGATGCCCCGGTCGTCGACGTCGGCCAGGTTGTTGAAGACAAACATCAGGTCTTCGATCTGCTCCGACAGGTCGCTGTCGATTTCACGGATCGCGTCCAT  >  NC_002947/4957757‑4958036

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: ‑