Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	780,758	T→C	100%	intergenic (+129/‑7)	lysT → / → valT	tRNA‑Lys/tRNA‑Val

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	780,758	0	T	C	98.5%	207.6 / ‑4.4	64	intergenic (+129/‑7)	lysT/valT	tRNA‑Lys/tRNA‑Val
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (30/33);  total (30/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.81e-01

AAGGATAACGTTGCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGTAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCA  >  NC_000913/780661‑780837                                                                                                  |                                                                                aaGGATAACGTTGCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGGGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCgcag                                                                               <  2:1611312/100‑1 (MQ=255)      tAACGTTGCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCg                                                                          >  1:2316635/1‑100 (MQ=255)         cGTTGCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGt                                                                       >  1:45125/1‑100 (MQ=255)         cGTTGCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGt                                                                       <  2:762232/100‑1 (MQ=255)             gCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTCACATAGTTAGTTCTAGTATCAAGCGCAGTATCAGATGa                                                                     >  2:21631/1‑98 (MQ=18)             gCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGAtt                                                                   >  1:1548788/1‑100 (MQ=255)              cATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTa                                                                  <  1:240857/100‑1 (MQ=255)              cATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTa                                                                  <  1:1210194/100‑1 (MQ=255)               aTGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAg                                                                 <  2:568605/100‑1 (MQ=255)               aTGAGCAACGGCCCGAAGGGCCAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAg                                                                 <  2:276978/100‑1 (MQ=255)                  aGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTc                                                              <  1:1756750/100‑1 (MQ=255)                   gCAACGGCCCGTAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCCCCACTATAAGAGTTAGGTGTAGAACCCAGCACAGTATCGTGTGGTTAg                                                                 >  2:1830735/1‑96 (MQ=12)                   gCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATACAGCGCAGTAGCGGGTGATTAGCTCa                                                             >  1:2350493/1‑100 (MQ=255)                   gCAACGGCCCGAAGGGCGAGACGAAGTCGAGACATCCTGCACGACCCACCACTAACATAGATAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCa                                                             >  1:1969569/1‑100 (MQ=255)                      aCGGCCCGAAGGGAGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGTAGTATCGGGTGATTAGCTCAGCt                                                          <  2:404355/100‑1 (MQ=255)                        ggCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTgg                                                        <  1:2137128/100‑1 (MQ=255)                         gCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTggg                                                       >  1:1368554/1‑100 (MQ=255)                          cccGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGga                                                      <  1:1954093/100‑1 (MQ=255)                             gAAGGGCGAGACGAAGTCGAGTCATCCTTCATGACCCTCCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGTTGATTAGCTCAGCTGGgag                                                     <  2:631906/98‑1 (MQ=25)                               aGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCa                                                 <  2:1962580/100‑1 (MQ=255)                               aGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCa                                                 <  1:1693874/100‑1 (MQ=255)                                gggCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCAc                                                <  2:2005746/100‑1 (MQ=255)                                 ggCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCAcc                                               <  1:1857345/100‑1 (MQ=255)                                   cGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTc                                             >  2:7549/1‑100 (MQ=255)                                   cGAGACGAAGTCGAGTCATCAAGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAATAACGGAAAATTAGCACAGCTGGGAGAGCACCTc                                             >  2:728769/1‑100 (MQ=25)                                    gagaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTcc                                            <  2:2348350/100‑1 (MQ=255)                                    gagaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTcc                                            <  1:1808551/100‑1 (MQ=255)                                    gagaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTcc                                            >  1:1382239/1‑100 (MQ=255)                                     agaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTccc                                           >  2:1655231/1‑100 (MQ=255)                                     agaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTccc                                           >  2:618456/1‑100 (MQ=255)                                     agaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAATCGGTTGTACGATGCAGCGCAGTATCGGGTGATGAGCTCAGCTTGGCGAGGCCCTcgc                                           >  2:1449457/1‑98 (MQ=16)                                      gaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt                                          <  1:139592/100‑1 (MQ=255)                                      gaCGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTGAGTTGTGGTATCCAGCGCAATATCGAATGATTAGCTCAGCTGGGAGAGCACGTcgc                                           >  2:1241660/1‑97 (MQ=25)                                         gAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTAc                                       <  2:2337014/100‑1 (MQ=255)                                          aaGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACa                                      <  1:659548/100‑1 (MQ=255)                                           caggttcgaaTCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACaa                                     <  2:896669/91‑1 (MQ=18)                                           aGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACaa                                     <  2:526350/100‑1 (MQ=255)                                            gTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAag                                    <  2:674706/100‑1 (MQ=255)                                               gAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAaggag                                 >  1:105227/1‑100 (MQ=255)                                                 gTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAggg                               <  1:1378281/100‑1 (MQ=255)                                                    aTCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGt                            >  1:981594/1‑100 (MQ=255)                                                    aTCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGt                            <  2:1548777/100‑1 (MQ=255)                                                    aTCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGt                            >  1:1171089/1‑100 (MQ=255)                                                     tCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTc                           <  2:1129487/100‑1 (MQ=255)                                                       cTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAggggggc                           >  2:922639/1‑96 (MQ=255)                                                        tGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTcggc                        >  1:1395392/1‑100 (MQ=255)                                                         gCACGACCCACCACTAATATAGTTAGTTGTAGTATTCAGCGCAGTATCGTGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTcggcg                       >  2:1070423/1‑100 (MQ=17)                                                         gCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTcggcg                       >  1:2199930/1‑100 (MQ=255)                                                         gCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTcggcg                       >  1:1939162/1‑100 (MQ=255)                                                          cACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTcggcgg                      >  2:712553/1‑100 (MQ=255)                                                           aCGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGt                     <  2:2014790/100‑1 (MQ=255)                                                            cGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGCCGGCGGtt                    >  1:1799566/1‑100 (MQ=255)                                                             gACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTc                   <  2:2316614/100‑1 (MQ=255)                                                             gACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTc                   <  1:1655244/100‑1 (MQ=255)                                                               cccACCACTAACATAGTTCGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACACGGAGGGGGTCGGCGGTTCGa                 >  1:144408/1‑100 (MQ=255)                                                               cccACCACTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGATCAGCTGGGCGAGCAGCTCCCTTAGAAGGAGGGGGTCGGCGGTTCGa                 >  2:1611840/1‑100 (MQ=17)                                                                ccaccaCTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGAt                <  1:7549/100‑1 (MQ=255)                                                                 caccacTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATc               <  1:2372350/100‑1 (MQ=255)                                                                    cacTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCg            <  1:232355/100‑1 (MQ=255)                                                                      cTAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGtc          <  1:1134659/100‑1 (MQ=255)                                                                       tAACATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGtca         <  1:2224538/100‑1 (MQ=255)                                                                        aaCATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGtcat        >  2:2375023/1‑100 (MQ=255)                                                                          cATAGTTAGTTGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGtcatc       <  2:2210680/99‑1 (MQ=25)                                                                              gttagttGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATcaccca  >  1:122513/1‑100 (MQ=11)                                                                              gttagttGTAGTATCCAGCGCAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATcaccca  >  2:1848732/1‑100 (MQ=11)                                                                                                  |                                                                                AAGGATAACGTTGCATGAGCAACGGCCCGAAGGGCGAGACGAAGTCGAGTCATCCTGCACGACCCACCACTAACATAGTTAGTTGTAGTATCCAGCGTAGTATCGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCA  >  NC_000913/780661‑780837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑