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	95.3%	115.6 / ‑2.6	44	S152* (TCA→TAA)	b4555	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  major base A (22/19);  minor base T (2/0);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 4.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

ACGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑A‑AAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTTGTG  >  NC_000913/4008297‑4008432                                                                             |                                                                      aCGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGCTGGCGGGGGGCGTTTc                                                                        >  2:1591342/1‑76 (MQ=255) aCGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTc                                                                        <  2:3715982/76‑1 (MQ=255)   gCTGGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑a‑a                                                                    <  2:3907418/76‑1 (MQ=255)    cTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGGTTC‑a‑aa                                                                   >  1:1162342/1‑76 (MQ=255)      cGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑a‑aaag                                                                 >  1:3045707/1‑74 (MQ=255)       gTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑a‑aaagg                                                                <  1:4625279/76‑4 (MQ=255)       gTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGGTTC‑a‑aaagg                                                                >  2:2092070/1‑73 (MQ=255)          ggggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGGGGCGGTTCAA‑AAGGCCa                                                              >  1:3126153/1‑76 (MQ=255)          ggggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCTA‑AAGGCCa                                                              >  1:3221371/1‑76 (MQ=255)          ggggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCa                                                              <  2:2188644/76‑1 (MQ=255)           gggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCAt                                                             <  1:2584076/76‑1 (MQ=255)           gggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCAt                                                             <  1:652289/76‑1 (MQ=255)            ggCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATg                                                            <  1:333893/76‑1 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgc                                                           <  1:1623184/76‑1 (MQ=255)             gCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgc                                                           <  2:3219923/76‑1 (MQ=255)              cGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgcg                                                          >  2:2213305/1‑76 (MQ=255)              cGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgcg                                                          >  2:2480022/1‑76 (MQ=255)               gATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGGGGCGGTTCAA‑AAGGCCATgcgc                                                         >  1:3448801/1‑76 (MQ=255)               gATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgagc                                                         <  1:1132992/76‑4 (MQ=255)               gATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCACgcgc                                                         >  2:4205222/1‑76 (MQ=255)               gATCGCGTCAACCTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgccc                                                         >  2:3760596/1‑74 (MQ=255)               caTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATgcgc                                                         >  2:3575133/2‑76 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGACGCGATGGCGGGAGGCGGTTCTA‑AACACCACGCGCt                                                        >  1:2481421/1‑76 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCt                                                        >  1:2714720/1‑76 (MQ=255)                aTCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAAGCCATGCGCt                                                        >  1:2153936/1‑76 (MQ=255)                 tCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTg                                                       <  2:1803275/76‑1 (MQ=255)                 tCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAAGCCATGCGCTg                                                       >  1:1822727/1‑76 (MQ=255)                   gcgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAAGCCATGCGGTGGa                                                     >  1:3852194/1‑76 (MQ=255)                   gcgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGGTTCAA‑AAGGCCCTGCGCTGGa                                                     >  1:2041518/1‑76 (MQ=255)                    cgTCAACGTCAGTTTCTCTCCCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGaa                                                    <  1:4414623/76‑1 (MQ=255)                    cgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGaa                                                    >  1:4375132/1‑76 (MQ=255)                    cgTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGaa                                                    <  2:4173395/76‑1 (MQ=255)                     gTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAg                                                   <  1:3090775/76‑1 (MQ=255)                      tCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGGGTTTC‑ACAAGGCCATGCGCCGGGAg‑g                                                 >  2:4793629/1‑76 (MQ=255)                      tCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAgc                                                  <  2:1270364/76‑2 (MQ=255)                      tCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAgc                                                  <  1:2762800/76‑2 (MQ=255)                      tCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAgc                                                  <  1:3251439/76‑2 (MQ=255)                       cAACGTCAGTTTCTCTACCTTCACCTGTCTGGAAGTGATGGCGGGCGGCGGTTCAA‑AAGGCCATGCGCTGGAAgcg                                                 >  1:584667/1‑74 (MQ=255)                       cAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAgcg                                                 >  1:582257/1‑74 (MQ=255)                               gTTTCTCTGCCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGCTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aa                                     <  2:1973290/76‑1 (MQ=255)                               gTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aa                                     <  2:4634551/76‑1 (MQ=255)                                tttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAgcgg                                                <  1:3729064/68‑4 (MQ=255)                                tttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGCTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aag                                    >  2:4349596/1‑75 (MQ=255)                                 ttCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aaga                                   <  1:4796033/76‑3 (MQ=255)                                 ttCTCTACCGTAACCGGTCTGGAAGTGATGGCGGGCGGCGTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑aaga                                   <  2:4594680/76‑3 (MQ=255)                                                                     ggcgTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg   >  1:2069/1‑74 (MQ=255)                                                                     ggcgTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttg   >  1:538722/1‑74 (MQ=255)                                                                      gcgTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg  >  2:3764795/1‑73 (MQ=255)                                                                      gcgTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg  >  1:3856558/1‑73 (MQ=255)                                                                      gcgTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg  >  2:3326156/1‑73 (MQ=255)                                                                      gcgTTTCAA‑AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGCGtttgg  >  2:2019842/1‑73 (MQ=255)                                                                             |                                                                      ACGCTCGTTGGGGCGATCGCGTCAACGTCAGTTTCTCTACCTTAACCTGTCTGGAAGTGATGGCGGGCGGCGTTTC‑A‑AAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTTGTG  >  NC_000913/4008297‑4008432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑