Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,797,772	G→C	100%	R7G (CGC→GGC)	USA300HOU_1679 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,797,772	0	G	C	100.0%	74.2 / NA	25	R7G (CGC→GGC)	USA300HOU_1679	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (16/9);  total (16/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCA  >  CP000730/1797636‑1797901                                                                                                                                         |                                                                                                                                  taaatcTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCcgtgg                                                                                                                               <  1:76612/141‑1 (MQ=255)      ttattgtCTTGCATCTGTTGCTAGAGCTTGGTCGTGTATTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGaaa                                                                                                                          <  2:57783/135‑1 (MQ=255)        atGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACt                                                                                                                        >  1:186780/1‑141 (MQ=255)             cTTGCATCTGTTTCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtcatc                                                                                                                   <  2:376775/141‑1 (MQ=255)                gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                >  1:239011/1‑141 (MQ=255)                 cATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATCAAACATATGTGCTGGAAGCGTGAATAATAGTGCCTAAGGTAACAAAACTGATAATTAATCTACTGCTTTTCTATAACATTAAGCCGTGGTGAGACTTGATCAttt                                                                                                               >  1:343600/1‑140 (MQ=255)                          cTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAATCTTAAGCCGTGGTGAAACTTCATCATTCTTCTTTAgg                                                                                                      >  2:262259/1‑141 (MQ=255)                                     tCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAtt                                                                                           >  1:147858/1‑141 (MQ=255)                                      cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTTTTTCCAAttt                                                                                          >  2:254302/1‑141 (MQ=255)                                      cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACAATAAGCCGGGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAttt                                                                                          >  1:164438/1‑141 (MQ=255)                                         gtTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTtata                                                                                       >  1:244803/1‑141 (MQ=255)                                                tgttAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAg                                                                                <  1:20785/138‑1 (MQ=255)                                                    aaaaCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCAc                                                                            <  1:225387/141‑1 (MQ=255)                                                      aaCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGGTAAGTAATATACTGCTTATCAATAACATTAAGCCGTGGAGAAACTCCATCAGTGTTCTTCAGGCATTTCCAATTTATAGACTAAGcaagcc                                                                          >  2:11549/1‑136 (MQ=255)                                                         atatGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTTTAGCCTAAGCCACGcaca                                                                       >  1:76343/1‑141 (MQ=255)                                                          tatCTGAGGGAAGCGAGGACAATAAGGCCTAATGTAACATAACTGAAAAATAATTTGCTACGGATAATTTACATTTAGCCGGTTTTTAACTTCAGCATTGTTCTTTAGGTCTTTCCGATTTATAGCCTAAGCCACGCACAg                                                                      <  2:62743/141‑1 (MQ=255)                                                                                                aaatCTGATAATTAATATGCTGCTTTGCAATAACATTAAGCCGTGGGTAAACTTCATCCTTGTTCTTTAGGTCTTTCTAATTTATAGCCTAAGCTACGCACAGTTTTAATAAGGTGTGGCTTCTTAGGATTATCTTCTAAt                                <  2:44139/141‑1 (MQ=255)                                                                                                aaaaCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAACCCACTCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAAt                                <  2:80938/141‑1 (MQ=255)                                                                                                      gATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtct                          >  2:193952/1‑141 (MQ=255)                                                                                                       aTAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtctc                         >  2:158200/1‑141 (MQ=255)                                                                                                               tataCTGCTTATAAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTATGATTATGTTCTAATTTATCTTTTAAATGa                 >  2:172825/1‑141 (MQ=255)                                                                                                                       ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg         >  2:288448/1‑141 (MQ=255)                                                                                                                        tATCAATAACATTAAGCCGTGGTGAAACTTCATCATCGTTCTTTAGGTCTTTCCTATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATATCTTAAATGACTGATATGt        <  1:213816/141‑1 (MQ=255)                                                                                                                             aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTCCATc   >  2:380747/1‑141 (MQ=255)                                                                                                                             aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATAACTGAAATGTACATc   >  2:215055/1‑141 (MQ=255)                                                                                                                              tAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATca  <  2:186780/141‑1 (MQ=255)                                                                                                                                         |                                                                                                                                  TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCA  >  CP000730/1797636‑1797901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑