Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,632,949	C→T	A20A (GCC→GCT)	ynfT →	Qin prophage; protein YnfT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,632,949	0	C	T	100.0%	117.7 / NA	51	A20A (GCC→GCT)	ynfT	Qin prophage; protein YnfT
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/21);  total (30/21)

CTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATA  >  NC_000913/1632822‑1633051                                                                                                                                |                                                                                                       cTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTa                                                                                            <  2:293606/140‑1 (MQ=25)    tAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAggg                                                                                         >  2:62300/1‑140 (MQ=21)     aaGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGa                                                                                        <  2:499073/140‑1 (MQ=21)            cccAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCat                                                                                 >  2:861167/1‑140 (MQ=21)             ccAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCata                                                                                <  1:826279/140‑1 (MQ=25)                      aaaTTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAAc                                                                       <  2:715547/140‑1 (MQ=17)                      aaaTTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAAc                                                                       <  1:861167/140‑1 (MQ=17)                       aaTTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAAcc                                                                      <  1:62300/140‑1 (MQ=17)                                   tatCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCg                                                          <  2:438674/140‑1 (MQ=14)                                          tataACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGtata                                                   >  2:383269/1‑140 (MQ=18)                                               cacaTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCa                                              >  1:1006851/1‑140 (MQ=18)                                               cacaTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCa                                              >  1:153714/1‑140 (MQ=18)                                               cacaTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCa                                              >  2:473689/1‑140 (MQ=18)                                               cacaTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCa                                              >  2:542097/1‑140 (MQ=18)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGGATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACa                                           >  1:587093/1‑140 (MQ=18)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGta                                                     >  1:1125477/1‑130 (MQ=18)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGta                                                     <  1:515214/130‑1 (MQ=14)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGta                                                     >  2:515214/1‑130 (MQ=21)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGta                                                     <  2:1125477/130‑1 (MQ=14)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTc                                               <  1:552425/136‑1 (MQ=14)                                                  aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTc                                               >  2:552425/1‑136 (MQ=18)                                                    tACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACata                                         >  1:540557/1‑140 (MQ=18)                                                    tACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACata                                         >  2:537890/1‑140 (MQ=18)                                                      cTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGGATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATc                                       <  2:587093/140‑1 (MQ=17)                                                         aTTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAg                                                 <  2:468043/127‑1 (MQ=17)                                                         aTTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAg                                                 >  1:468043/1‑127 (MQ=17)                                                         aTTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTg                                    >  2:222543/1‑140 (MQ=18)                                                         aTTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTg                                    <  1:222543/140‑1 (MQ=17)                                                            cGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAAt                                 >  2:639487/1‑140 (MQ=18)                                                            cGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAAt                                 >  2:64304/1‑140 (MQ=18)                                                            cGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAAt                                 >  1:599678/1‑140 (MQ=18)                                                             gAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATc                                <  2:540557/140‑1 (MQ=17)                                                             gAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATc                                <  2:914838/140‑1 (MQ=17)                                                              aGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACa                                           <  2:416601/128‑1 (MQ=14)                                                              aGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACa                                           >  1:416601/1‑128 (MQ=18)                                                              aGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCa                               >  2:852465/1‑140 (MQ=18)                                                              aGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCa                               <  1:383269/140‑1 (MQ=17)                                                               ggCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAg                              <  1:852465/140‑1 (MQ=17)                                                               ggCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCACATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAg                              <  2:1066652/140‑1 (MQ=17)                                                                    tatGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATa                         >  1:328822/1‑140 (MQ=18)                                                                    tatGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATa                         >  1:396482/1‑140 (MQ=18)                                                                     atGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATAc                        >  1:424089/1‑140 (MQ=18)                                                                         aCAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAata                    >  1:377832/1‑140 (MQ=18)                                                                          cAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAatat                   <  2:424089/140‑1 (MQ=17)                                                                           aGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATc                  >  1:1062692/1‑140 (MQ=18)                                                                              aTACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCa               >  2:395013/1‑140 (MQ=18)                                                                                     tAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGaaaa        >  1:343893/1‑140 (MQ=18)                                                                                       aTCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATc      >  2:634003/1‑140 (MQ=18)                                                                                       aTCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATc      >  1:893819/1‑140 (MQ=18)                                                                                       aTCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATc      >  2:447301/1‑140 (MQ=18)                                                                                           caTCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCaata  <  2:755633/140‑1 (MQ=14)                                                                                                                                |                                                                                                       CTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATA  >  NC_000913/1632822‑1633051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑