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	94.9%	109.9 / ‑5.7	41	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base A (20/17);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 4.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAA  >  NC_000913/4184406‑4184673                                                                                                                                          |                                                                                                                                   ggcccttACACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGCTAACAAGGGTGTAATTTCTAAGACCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                               <  1:217384/138‑1 (MQ=255) ggCGGGTAAGCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                               <  2:832475/143‑1 (MQ=255)    ggTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCCGTAGACACCGTACAGAACCGACGGGGCg                                                                                                                            >  2:455132/1‑143 (MQ=255)         aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAAGCGGCGGGGCGtcgcg                                                                                                                       >  1:584368/1‑139 (MQ=255)         aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGCAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTAATGAACGAGCTGGGCGTGCCg                                                                                                                       >  1:106443/1‑143 (MQ=255)           cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGcgcggaacgcc                                                                                                                     >  2:516589/1‑136 (MQ=255)                             gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCa                                                                                                   >  1:395035/1‑143 (MQ=255)                              aCAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAg                                                                                                  >  1:178088/1‑143 (MQ=255)                                  gATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTCTGTACATCGTTCTGCTcc                                                                                              >  1:14545/1‑143 (MQ=255)                                   attgCAGGTCGTCGCGGTAACAAGGGTGTAAGTTCTAAGATCACCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                             <  1:346898/140‑1 (MQ=255)                                        aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGCAAACGGTACGCCGGGAGACATCGTACTGAACCCGCTGGGCGTCCCGTCTCGTCTGACCACCGGACCGCTCCCCGaca                                                                                        >  2:232009/1‑141 (MQ=255)                                                aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGCTCCTCGAAAccccccgg                                                                                >  1:883406/1‑141 (MQ=255)                                                  ggTAACATGGGTGTAATTTCGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                              <  2:474648/143‑1 (MQ=255)                                                  ggTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                              <  1:912410/143‑1 (MQ=255)                                                   gcaaCAAGGTTGTAATTTCTACGATCAACCCGATCGAAGATATGCCTTACGATGAAGACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCTGTTAGATCCTCGAAACCCACCTGGGt                                                                             <  2:903209/141‑1 (MQ=255)                                                        aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCGGGTCTGGc                                                                        >  2:633025/1‑143 (MQ=255)                                                               tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                 <  2:826333/143‑1 (MQ=255)                                                                 aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGCCCCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTCCGACAgg                                                               >  2:684894/1‑143 (MQ=255)                                                                     ccaagcacAACCCGATCGAAGATAGGCCTTACGATGAAAACGGTACGCCGGTAGTCTGCCTACTATACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATc                                                           <  1:666229/136‑1 (MQ=255)                                                                           tCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                     >  1:191099/1‑143 (MQ=255)                                                                             aaccgcaTCGACGAGATGCCGTACGATGGAAACGGTACGGCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                   <  2:294856/137‑1 (MQ=255)                                                                             aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGATCCTCGCAACCCACCTGCGTATGGCTGCGAAAGGTATCGGCGACaa                                                   >  2:479079/1‑143 (MQ=255)                                                                               cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                 >  1:737210/1‑143 (MQ=255)                                                                                ccGATCGAAGAGATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCGCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAt                                                <  2:106904/143‑1 (MQ=255)                                                                                    tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCGCACTGGGTATGGCTGCGAAAGGTAGCGGCGCCAAGATCCAc                                            >  2:662548/1‑143 (MQ=255)                                                                                     cGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCCACCCCCCTGGGTATGGCTGCGAAAGGTATCGGCCACAAGATCAACg                                           >  1:271254/1‑143 (MQ=255)                                                                                      gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACACGATAGACGc                                          >  1:242278/1‑143 (MQ=255)                                                                                              gCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGTTCAGATCCTCGAAACCCACCTGGGGATGGCTGCGCAAGGTCTCCGCGACCAGATCAAAGCCATGCTGa                                  >  2:518076/1‑143 (MQ=255)                                                                                              gCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                  >  1:474983/1‑143 (MQ=255)                                                                                                gttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                <  1:326553/142‑1 (MQ=255)                                                                                                 ttACGATGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                               <  1:598173/143‑1 (MQ=255)                                                                                                   aCGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGACACCCACCTGGGTATGGCTGCGGCAGGTATCGGCGCCCAGGTCACCGCCATGCTGAAAcag                             >  1:37662/1‑143 (MQ=255)                                                                                                   aCGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcag                             >  1:321966/1‑143 (MQ=255)                                                                                                     gATGAAAACGGTCCGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTATCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcagca                           <  1:908775/143‑1 (MQ=255)                                                                                                     gATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGCTGAACGCAATGCTGAAAcagca                           >  1:225848/1‑143 (MQ=255)                                                                                                       tGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACagcagc                         <  1:490919/143‑1 (MQ=255)                                                                                                         accaCGGTCCGCCGGTAGACATCGTACTGAACCAGCGGGGCTTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                       <  1:120606/140‑1 (MQ=255)                                                                                                               gTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTc                 >  1:540931/1‑143 (MQ=255)                                                                                                                   gCCGGTAGACATCGCACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa             <  1:521128/143‑1 (MQ=255)                                                                                                                             aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCACATCGGTCAGATCCGCGAGACCCACCCGGCTATGCCTGCGACAGGTACCGGCGACCACATCAACCCCATGCCGCAGCAGCAGCCACCCGCCGCGAAAcaccccca   >  2:95938/1‑136 (MQ=255)                                                                                                                              tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa  <  1:893225/143‑1 (MQ=255)                                                                                                                                          |                                                                                                                                   GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAA  >  NC_000913/4184406‑4184673

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: ‑