Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,008,375	+A	coding (458/516 nt)	b4555 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,008,372	1	.	A	93.5%	134.3 / 3.1	46	coding (455/516 nt)	b4555	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (3/0);  new base A (11/32);  total (14/32)
Fisher's exact test for biased strand distribution p-value = 2.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTTGTG  >  NC_000913/4008297‑4008432                                                                               |                                                                     aCGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTc                                                                       <  1:2264333/76‑1 (MQ=255) aCGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTc                                                                       <  1:2319482/76‑1 (MQ=255) aCGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTc                                                                       <  2:258788/76‑1 (MQ=255)  cGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTC‑a                                                                     <  2:5783786/76‑1 (MQ=255)    cTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTC‑caa                                                                   >  2:4096737/1‑76 (MQ=255)     tCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGACGTGATGGCGGGCGG‑CG‑TTTC‑aaaa                                                                  <  1:1574571/76‑2 (MQ=255)     tCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTC‑aaaa                                                                  >  2:3584822/1‑75 (MQ=255)      cGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑GTTC‑aaaag                                                                 >  1:1601882/1‑74 (MQ=255)         tGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGTCGGGCGG‑CG‑GTTC‑CAAAGcgc                                                              >  2:1105603/1‑74 (MQ=255)          ggggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCAGTCTGGAAGTGATGGCGGGCGGCCT‑TTTC‑AAAAGCCa                                                              >  2:1735251/1‑76 (MQ=255)           gggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCAt                                                             <  2:2426963/76‑1 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATgc                                                           <  1:1401312/76‑1 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATgc                                                           <  2:842396/76‑1 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATgc                                                           >  1:2210680/1‑76 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑GTTCAAAAGGCCATgc                                                           >  1:3197258/1‑76 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑GTTCAAAAGGCCATgc                                                           >  2:2014725/1‑76 (MQ=255)               gATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATgcgc                                                         >  1:4472167/1‑76 (MQ=255)               gATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAAGCCATgcgc                                                         >  2:1039579/1‑76 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGGGG‑CG‑GTTCAAAAAGCCATgcgcg                                                        >  1:683837/1‑75 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCt                                                        <  1:155714/76‑1 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCt                                                        <  1:5639231/76‑1 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCt                                                        <  1:5521837/76‑1 (MQ=255)                 tCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTg                                                       <  2:3284386/76‑1 (MQ=255)                 tCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTg                                                       <  2:3884858/76‑1 (MQ=255)                  cgcgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTgg                                                      <  1:3584822/76‑1 (MQ=255)                   gcgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGa                                                     <  2:940411/76‑1 (MQ=255)                   gcgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGa                                                     <  1:5600575/76‑1 (MQ=255)                   gcgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGa                                                     <  1:295348/76‑1 (MQ=255)                   gcgTCAACGTCAGTCTGTCTACATTCACCTGTCTGGAAGTGATGGAGGCCGG‑CG‑TTTCAAAATGCCAGGCGCTGGa                                                     <  1:282784/76‑1 (MQ=255)                    cgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGaa                                                    >  1:3415444/1‑76 (MQ=255)                    cgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGaa                                                    <  1:3518617/76‑1 (MQ=255)                     gTCGACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAg                                                   <  2:5578868/76‑1 (MQ=255)                     gTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CGTTTTA‑AAAAGCCATGCGCTGGGAg                                                   >  1:4762621/1‑76 (MQ=255)                     gTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAg                                                   <  1:3531462/76‑1 (MQ=255)                      tCATCGTCAGTTGCTCTACCTTACCCTGTCTGGACGTGATGGCGGTCGG‑CT‑TTTCAAAATGCCATGCGCTGGacgc                                                  <  1:4002659/76‑4 (MQ=255)                      tCATCGTCAGTTGCTCTACCTTACCCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAgc                                                  <  1:3964125/76‑2 (MQ=255)                      tCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAgc                                                  <  1:4875979/76‑2 (MQ=255)                       cAACGTCAGTTTCTCTACCTTAGCCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAgcg                                                 <  2:3148274/76‑3 (MQ=255)                       cAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAgcg                                                 <  2:2371275/76‑3 (MQ=255)                       cAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAgcg                                                 <  1:2302911/76‑3 (MQ=255)                       cAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAgcg                                                 <  1:4163196/76‑3 (MQ=255)                        aaCGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAAGCCATCCCCCGGAAg‑ggg                                               >  2:586117/1‑74 (MQ=255)                               gTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGaa                                                    <  2:61007/65‑1 (MQ=255)                               gTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGaa                                                    >  1:61007/1‑65 (MQ=255)                                tttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aag                                    <  2:4415745/76‑2 (MQ=255)                                tttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aag                                    >  2:2872272/1‑75 (MQ=255)                                 ttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aaga                                   <  1:5258628/76‑3 (MQ=255)                                 ttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aaga                                   <  1:1105603/76‑3 (MQ=255)                                  tctcTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aagaa                                  <  2:4149562/76‑4 (MQ=255)                                  tctcTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aagaa                                  <  2:2142419/76‑4 (MQ=255)                                                                    cgg‑cg‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGttt    <  1:3155074/76‑2 (MQ=255)                                                                     gg‑cg‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg   >  2:2714591/1‑74 (MQ=255)                                                                      g‑cg‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg  <  1:4395452/76‑4 (MQ=255)                                                                      g‑cg‑TTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg  <  1:1469210/76‑4 (MQ=255)                                                                               |                                                                     ACGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGG‑CG‑TTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTTGTG  >  NC_000913/4008297‑4008432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑