Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,642,961	T→C	Y94C (TAC→TGC)	ydfT ←	Qin prophage; putative antitermination protein Q

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,642,961	0	T	C	100.0%	130.8 / NA	37	Y94C (TAC→TGC)	ydfT	Qin prophage; putative antitermination protein Q
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/19);  total (18/19)

TTACAGATTCCCCGCGTCTGTAGTGTTTCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGTAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGAGGGTCCTGAACACCAACTTTTGCCAGAAATAAGG  >  NC_000913/1642827‑1643093                                                                                                                                       |                                                                                                                                     ttACAGATTCCCCGCGTCTGTAGTGTTTCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGAAAAGGCAAAACTCACGAGGCAAGGa                                                                                                                                 >  1:267432/1‑140 (MQ=255)  tACAGATTCCCCGCGTCTGTAGTGTTTCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGaa                                                                                                                                <  1:484750/140‑1 (MQ=255)  tACAGATTCCCCGCGTCTGTAGGGTTTCAACACTTCGGGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTG‑CGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGaat                                                                                                                               <  1:263525/140‑1 (MQ=255)               cgTCTGTAGTGTTTCCCCACTTAGCTCAAAACATTATCAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCg                                                                                                                   <  1:186772/140‑1 (MQ=255)                       gtgtTTCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAGCTCACGAGGCAAGGAATAATCTGTAACCGGATttctt                                                                                                           <  2:498790/140‑1 (MQ=255)                          tttCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCAc                                                                                                        <  2:121420/140‑1 (MQ=255)                          tttCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCAc                                                                                                        >  1:422910/1‑140 (MQ=255)                          tttCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCAc                                                                                                        >  1:360720/1‑140 (MQ=255)                               ccacTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAAt                                                                                                   <  2:351867/140‑1 (MQ=255)                               ccacTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAAt                                                                                                   <  1:394530/140‑1 (MQ=255)                                    tCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGtt                                                                                              <  2:667345/140‑1 (MQ=255)                                         cAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATg                                                                                         <  2:267432/140‑1 (MQ=255)                                              cATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCggg                                                                                    <  2:128641/140‑1 (MQ=255)                                                 tataAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTa                                                                                 >  2:506810/1‑140 (MQ=255)                                                    aaaaTCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATcc                                                                              >  1:144092/1‑140 (MQ=255)                                                      aaTCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAg                                                                            >  2:427823/1‑140 (MQ=255)                                                      aaTCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAg                                                                            >  2:360199/1‑140 (MQ=255)                                                        tCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTg                                                                          >  1:368915/1‑140 (MQ=255)                                                        tCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCGGTAACCGGCTTTCTTCCCTCAATTTGTTCAATGTCGGGTTATCCAGTg                                                                          >  2:271339/1‑140 (MQ=255)                                                           cGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATg                                                                                         <  1:658842/122‑1 (MQ=255)                                                           cGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATg                                                                                         >  2:658842/1‑122 (MQ=255)                                                             tACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATc                                                                     >  1:105703/1‑140 (MQ=255)                                                             tACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAAACGGATTTCCTCATTCAATTTGTTCATTGTCGGGTTATCCAGTGCCATc                                                                     >  2:296266/1‑140 (MQ=255)                                                              aCCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATcg                                                                    <  1:37513/140‑1 (MQ=255)                                                                        tGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAg                                                          >  1:570968/1‑140 (MQ=255)                                                                             acaGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGc                                                     >  1:401183/1‑140 (MQ=255)                                                                                gCGAGCCTTACTTGCCGCAGACATGAAGTCATCAGCACAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCtt                                                  <  1:181320/140‑1 (MQ=255)                                                                                   aGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCaa                                               >  1:119447/1‑140 (MQ=255)                                                                                         aCTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTAACCACTGCGATCGCGTAATTTAGCAGGCCTTCAATCGCaa                                         >  2:237127/1‑140 (MQ=255)                                                                                             gCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTg                                     >  1:146925/1‑140 (MQ=255)                                                                                              ccGCAGACCTGGAGTCATCAGCGAATGCATAACTCACCAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGa                                    <  1:237127/140‑1 (MQ=255)                                                                                              ccGCAGACCTGGAGTCATCAGCAAACGCAAAACTCACCAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGa                                    <  1:296266/140‑1 (MQ=255)                                                                                                                  gCAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGAGGGTCCTGAACACCAACttt                <  2:119447/140‑1 (MQ=255)                                                                                                                   cAAAGGCAAAACTCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTGCAATCGCAAACTTAGGGTCCTGAACACCAACtttt               >  2:211296/1‑140 (MQ=255)                                                                                                                               tCACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGAGGGTCCTGAACACCAACTTTTGCCAGAAATAAg   <  1:427823/140‑1 (MQ=255)                                                                                                                                cACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGAGGGTCCTGAACACCAACTTTTGCCAGAAATAAgg  <  1:154659/140‑1 (MQ=255)                                                                                                                                cACGAGGCAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGAGGGTCCTGAACACCAACTTTTGCCAGAAATAAgg  <  1:506810/140‑1 (MQ=255)                                                                                                                                       |                                                                                                                                     TTACAGATTCCCCGCGTCTGTAGTGTTTCACCACTTCGCGCAATACATTATAAAATCCCGTACCTGAACAATGCTCACAGCGAGCCTTACTTGCCGCAGACCTGGAGTAATCAGCAAAGGCAAAACTCACGAGGTAAGGAATAATCTGTAACCGGATTTCTTCACTCAATTTGTTCAATGTCGGGTTATCCAGTGCCATCGCGTAATTTAGCAGGCCTTCAATCGCAAACTGAGGGTCCTGAACACCAACTTTTGCCAGAAATAAGG  >  NC_000913/1642827‑1643093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑