Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	100.0%	185.1 / NA	58	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (29/29);  total (29/29)

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184681                                                                                                                                            |                                                                                                                                           cTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACCGAACCAGCt                                                                                                                                         >  2:207152/1‑143 (MQ=255)   ggCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                       <  2:639821/143‑1 (MQ=255)     cggtagaaCGCCGTATCCAGCCGGGTGACAGGAGGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCGAAGATCAACCCGATCGAAGATATGCCTGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                                     <  2:426530/137‑1 (MQ=255)     cGGTTAAACGCCGTATCCAGCCTGGTGACAGGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTACGATCAACCAGATCGAAGAGATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGc                                                                                                                                     <  2:544731/143‑1 (MQ=255)         gtagcGCCGTATCGAGCCGGGGGACACGATGGCAGGTCGTCACGGTAACAGGGGTGTTGTTGCGAAGATCACCCCGATCGAGGATATGCCGCACGATGATAACGGTACGCCGGGAGACGTCGTACTGAACCAGCTGGGCGTAc                                                                                                                                 <  2:292523/139‑1 (MQ=255)          aagcGCTGTATGCAGCCTGGTGACATGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTACGATCAACCCGATCGAAGATATGTCTTACGATGAAATCGGTACGCCGGTAGACTTCGTACTGAACCAGCTGGGCGTAcc                                                                                                                                <  2:138630/140‑1 (MQ=255)          aaaCGCGGTATCCAGGCTGGTGACAAGATGGCATGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCTAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAcc                                                                                                                                <  2:202773/143‑1 (MQ=255)            aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGt                                                                                                                              >  1:905186/1‑143 (MQ=255)              gCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtcc                                                                                                                            >  2:967071/1‑142 (MQ=255)               ccGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                           >  1:738180/1‑143 (MQ=255)               ccGTATCCAGCCTGGTCACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCGTACGATGAAAACGGTGCGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                           <  2:366912/143‑1 (MQ=255)                cGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCAATCGAAGATATACCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGACCCAGCTGGGCGTACCGTCTCg                                                                                                                          >  2:75282/1‑143 (MQ=255)                 ggagccAGCCTGGGGACAAGAGGGCAGGTCGGCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                         <  2:196331/139‑1 (MQ=255)                     ccAGGCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAGGATGTGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGa                                                                                                                     <  2:818510/143‑1 (MQ=255)                     ccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGACAACGGTACGCCGGGAGACATCGCACTGAACCAGCTGGGCGTACCGCCGCGTagaa                                                                                                                     >  2:862443/1‑140 (MQ=255)                       aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTCGACATCGACCTGACCCAGCGGGGCGTACCGTCCCGTAGGAAc                                                                                                                   >  2:616384/1‑143 (MQ=255)                           tGGTTACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTCATTTCTAAGATCAACCCGATCGAAGATATGCGTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCGGGGCGTACCGTCTCGTATGAACATCg                                                                                                               <  1:437603/143‑1 (MQ=255)                               gACAAGATGGCAGGTCGTCACGGCAACAAGGGTGTAATTTCGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                           <  2:909344/143‑1 (MQ=255)                                  aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGACGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGCCAGAt                                                                                                        >  1:460788/1‑143 (MQ=255)                                  aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACACCGGCCAGAt                                                                                                        >  1:952837/1‑143 (MQ=255)                                          aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                >  1:913476/1‑143 (MQ=255)                                                tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcc                                                                                          >  1:786774/1‑143 (MQ=255)                                                   cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                       <  1:741491/143‑1 (MQ=255)                                                    ggTAACAAGGGTGGAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                                      <  1:980308/143‑1 (MQ=255)                                                     gTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGt                                                                                     <  2:702249/143‑1 (MQ=255)                                                     gTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCGCGTATGAACATCGGTCAGATGCTCGAAGCCCACCtcgcg                                                                                     >  2:966642/1‑139 (MQ=255)                                                        gcgaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATg                                                                                  <  2:750120/140‑1 (MQ=255)                                                          aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACAGTACGCCGGTAGACATCGTACTGAACCAGCGGGGCGTACCGTATCGCATAAACCTCGGTCAGAGCCCCAAAACCCACCTGGGGATGGc                                                                                >  2:606971/1‑143 (MQ=255)                                                             ggTGGAATGTCTAAGACCAAGCCGATCGAAGATATGGCTTACGATGAAAACGGGACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGCCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                             <  1:293623/143‑1 (MQ=255)                                                             gctgaaaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAGAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                             <  2:328173/138‑1 (MQ=255)                                                                 tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                         <  1:626527/143‑1 (MQ=255)                                                                  ggttcccaaGAACAACCCGATGGGAGAGATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                        <  1:525021/136‑1 (MQ=255)                                                                  aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGACTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                        <  1:972550/143‑1 (MQ=255)                                                                    tttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGCCATCGTACTGAACCAGCTGGGCGTACCGTCTCGAATGAACATCGGTCAGATCCTCCAAACCCACCTGGGTATGGCTGCGAAAGGt                                                                      >  1:983915/1‑143 (MQ=255)                                                                     ttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGAGCGTACCGTCTCGTATGGACATCGGTCAGATCCTCGAAACCCACGCGGGTCTGGCTGCGGAAggga                                                                     >  1:562527/1‑141 (MQ=255)                                                                      tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGCTCCTCGACACCCACCAGGGTAAGGATgagacatatat                                                                    >  2:393100/1‑136 (MQ=255)                                                                         aaGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACACAACTGGGTATGGCTGCGAGAGGTATCgg                                                                 >  2:975554/1‑143 (MQ=255)                                                                          aGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGc                                                                <  2:894325/143‑1 (MQ=255)                                                                               aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                           >  2:977215/1‑143 (MQ=255)                                                                               aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTGCCGGCGAcca                                                           >  2:449590/1‑141 (MQ=255)                                                                                 cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                         >  1:800206/1‑143 (MQ=255)                                                                                 cccGATCGAAGATATGCCTGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                         <  1:433824/143‑1 (MQ=255)                                                                                      tCGAAGATATGCCTGACGATGAAAACGGTACGCCGGTAGACGTCGTACTGCACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                    <  1:463874/143‑1 (MQ=255)                                                                                         aaGATAGGACTGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTGAGGTCGTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGcc                                                 <  2:515044/143‑1 (MQ=255)                                                                                          aGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTCTCGGCGACAAGATCAATGCCa                                                >  1:623426/1‑143 (MQ=255)                                                                                              atGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTCTGGCTGCGAAAGGTGTCGGCGACCAGATCAACGCCCTGCt                                            >  2:965708/1‑143 (MQ=255)                                                                                                  cTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                        >  1:941394/1‑143 (MQ=255)                                                                                                    tgcgctGAAAGCGGTGCGCGGGTAGACACCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAca                                      <  2:1123973/138‑1 (MQ=255)                                                                                                         tGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACagcagc                                 >  1:787387/1‑143 (MQ=255)                                                                                                                  tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                        <  1:321697/143‑1 (MQ=255)                                                                                                                   aCGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgc                       >  1:659307/1‑143 (MQ=255)                                                                                                                   aCGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCGGGTATGGCTGCGAAAGGTATCGGCGACAGAACCAGCGCCAGGCCGACACAGCAGCcagcacgacc                       >  2:926008/1‑136 (MQ=255)                                                                                                                     gCCGGTACACATCGTCGTGAACCAGCTGGTCGTACCGTCTCGTATGAACATCGGGCAGACCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                     <  2:741089/143‑1 (MQ=255)                                                                                                                       cGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGaaa                   <  1:977215/143‑1 (MQ=255)                                                                                                                             aCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACAgcgc             >  1:681333/1‑143 (MQ=255)                                                                                                                                tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATAAACGCCCTGCTGACACAGCACGAAGAAGCCGCGACACTCCGCGaa          >  2:522536/1‑143 (MQ=255)                                                                                                                                 cGTACTGACCCAGCGGGGCGTTCCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCGCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt         <  2:197846/143‑1 (MQ=255)                                                                                                                                        aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCGAGAAGTCGCGAAACTGCGCGACTTCATCCa  >  1:1093584/1‑143 (MQ=255)                                                                                                                                            |                                                                                                                                           CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184681

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑