Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,976,605	T→C	F110L (TTT→CTT)	wzxE →	O‑antigen translocase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,976,605	0	T	C	97.1%	121.4 / ‑4.4	35	F110L (TTT→CTT)	wzxE	O‑antigen translocase
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (19/15);  total (20/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.53e-01

TACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑TTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAA  >  NC_000913/3976470‑3976720                                                                                                                                         |                                                                                                                    tACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTg                                                                                                                  >  2:456492/1‑139 (MQ=255)   cGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGt                                                                                                                >  1:66958/1‑139 (MQ=255)      tGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAAt                                                                                                             >  2:703416/1‑139 (MQ=255)                  tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGGTAATACCGACTATCa                                                                                                  >  2:561563/1‑139 (MQ=255)                  tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAg                                                                                                 >  1:581137/1‑139 (MQ=255)                  tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAg                                                                                                 >  2:660546/1‑139 (MQ=255)                  tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAg                                                                                                 >  1:580084/1‑139 (MQ=255)                       aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATAcc                                                                                                          >  2:277203/1‑125 (MQ=255)                       aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATAcc                                                                                                          <  1:277203/125‑1 (MQ=255)                       aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAgggg                                                                                              <  1:406141/137‑1 (MQ=255)                       aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAgggg                                                                                              >  2:406141/1‑137 (MQ=255)                       aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCt                                                                                            >  1:381030/1‑139 (MQ=255)                        tCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTg                                                                                           <  1:660546/139‑1 (MQ=255)                                  cTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAg                                                                                 <  1:456492/139‑1 (MQ=255)                                    gcgcCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTg                                                                               >  2:467429/1‑139 (MQ=255)                                         gcgTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCt                                                                          <  2:20018/139‑1 (MQ=255)                                            tGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGt                                                                       <  2:381030/139‑1 (MQ=255)                                             ggTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGTGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                      <  1:467429/139‑1 (MQ=255)                                             ggTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                      <  2:66958/139‑1 (MQ=255)                                                                aTGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTggg                                                   >  2:21294/1‑139 (MQ=255)                                                                 tGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTgggg                                                  <  1:703416/139‑1 (MQ=255)                                                                        tGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTg                                           >  1:51971/1‑139 (MQ=255)                                                                           tttCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGt                                                                                         >  1:667514/1‑90 (MQ=255)                                                                           tttCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGt                                                                                         <  2:667514/90‑1 (MQ=255)                                                                              ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTg                                     >  2:99866/1‑139 (MQ=255)                                                                              ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTg                                     >  2:732804/1‑139 (MQ=255)                                                                              ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTg                                     >  2:405761/1‑139 (MQ=255)                                                                                 tACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGgcg                                  <  2:4652/139‑1 (MQ=255)                                                                                        aTGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCtgatga                           >  2:274340/1‑139 (MQ=255)                                                                                                  tttttGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGa                                                                                                        >  2:279452/1‑52 (MQ=255)                                                                                                  tttttGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGa                                                                                                        <  1:279452/52‑1 (MQ=255)                                                                                                          cTGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCg         <  1:269700/139‑1 (MQ=255)                                                                                                           tGGCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGc        <  2:580084/139‑1 (MQ=255)                                                                                                            ggCAGCTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCa       >  1:481985/1‑139 (MQ=255)                                                                                                                 cTGCGCCAATCAGCCAGGGATTG‑CTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTaa  <  1:21294/139‑1 (MQ=255)                                                                                                                                         |                                                                                                                    TACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTG‑TTTGGTAATACCGACTATCAGGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAA  >  NC_000913/3976470‑3976720

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑