Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,482,396	A→G	L481P (CTG→CCG)	valS ←	valine‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,482,396	0	A	G	97.6%	139.7 / NA	41	L481P (CTG→CCG)	valS	valine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (24/16);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 4.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAAGTGCATGGTCATCATGATCATGCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACAGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGCCG  >  NC_000913/4482259‑4482531                                                                                                                                          |                                                                                                                                        tgaAGTGCATGGTCATCATGATCATGCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGgc                                                                                                                                       >  1:699290/1‑140 (MQ=255)        cATGGTCATCATGATCATGCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCagaag                                                                                                                                >  1:676300/1‑140 (MQ=255)        cATGGTCATCATGATCATGCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGCTCCACGGCGCagaag                                                                                                                                >  1:385593/1‑140 (MQ=255)             tcatcaTGATCATGCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAAc                                                                                                                           <  1:850908/140‑1 (MQ=255)             tcatcaTGATCATGCGGGCAATACATAAGTAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAAc                                                                                                                           <  1:296868/140‑1 (MQ=255)                tcatgatcatgCGGGCACTCCATAAGAAAATGAGGGCGAGACCAGATAGCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAg                                                                                                                        <  2:385593/140‑1 (MQ=255)                   tgatcatgCGGGCAACCCAGAAAAATATGATGTCGAATCCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTa                                                                                                                     <  1:288161/140‑1 (MQ=255)                       catgCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCga                                                                                                                 <  2:676300/140‑1 (MQ=255)                        atgCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCgag                                                                                                                >  1:825875/1‑140 (MQ=255)                          gCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGACAAGGGTAGAGATGGTCCACGGCGCCGAAGAGAACCAGGTATCGAGaa                                                                                                              >  2:288161/1‑140 (MQ=255)                          gCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGCTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGaa                                                                                                              >  2:82468/1‑140 (MQ=255)                               agaTCCAGAAGAAAATGCTTTCAAAACCAGAAACCATCAAGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCt                                                                                                         <  2:328757/138‑1 (MQ=255)                                  tCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCg                                                                                                      >  1:478310/1‑140 (MQ=255)                                          aaaaTGATGTCGAAACCCGATACCATCACGCTGGTAGGGGGGAACTGAAGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACg                                                                                              <  2:350283/140‑1 (MQ=255)                                            aaTGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGATGAGAACCGGGTATCCAGAACGTCTTCGTCCTGACGct                                                                                            >  1:328757/1‑139 (MQ=255)                                            aaTGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTcc                                                                                                   <  1:22354/133‑1 (MQ=255)                                            aaTGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTcc                                                                                                   >  2:22354/1‑133 (MQ=255)                                            aaTGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCa                                                                                            >  1:593879/1‑140 (MQ=255)                                             atgatgTCGAAACCAGATACCATCACGCTGGCTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAg                                                                                           <  1:82468/140‑1 (MQ=255)                                                atgTCGAAACCAGATACCATCACGCTGGTTGGTTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGac                                                                                        <  2:598152/140‑1 (MQ=255)                                                    cGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGacaaca                                                                                    <  1:685607/140‑1 (MQ=255)                                                           aGATACCATCACGCTGGTTGGGGGGAACTGAAGCAGGGCTTCGGTATTCTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCAc                                                                             <  2:367623/140‑1 (MQ=255)                                                                ccATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAgg                                                                        <  2:478310/140‑1 (MQ=255)                                                                    cACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTAACGGAGGACAACATCAGCACCGAGGTTAt                                                                    >  1:221700/1‑140 (MQ=255)                                                                           gTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCttt                                                             >  2:681390/1‑140 (MQ=255)                                                                           gTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAAAGTCTTCGTTCTGGCGCATGACAACATCAGCACCGAGGTTATTTTCttt                                                             >  2:412227/1‑140 (MQ=255)                                                                                              gggCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTg                                          >  1:518667/1‑140 (MQ=255)                                                                                                  gTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGc                                      <  2:593879/140‑1 (MQ=255)                                                                                                  gTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGc                                      <  2:825875/140‑1 (MQ=255)                                                                                                   tcagTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGcc                                     >  2:555671/4‑140 (MQ=255)                                                                                                   tCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGcc                                     >  1:478963/1‑140 (MQ=255)                                                                                                         ttttCCGGCCAGCCAAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATa                               >  1:111864/1‑140 (MQ=255)                                                                                                                    gccaAGGGTAGAGAATGTCCACAGCCCAGGAGAGAACGAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCg                    <  1:412227/140‑1 (MQ=255)                                                                                                                     ccaAGGGTAGAGAAGGTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGc                   <  1:555671/140‑1 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGGGGCCAACCTAAACGCTACCCGATTCGTCATACCATGc    >  1:413871/1‑140 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATg     <  1:710785/139‑1 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATg     >  2:710785/1‑139 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGc    >  2:552967/1‑140 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGc    >  2:661435/1‑140 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGc    >  2:701002/1‑140 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGc    >  2:726233/1‑140 (MQ=255)                                                                                                                                    gTCCACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGc    >  1:834161/1‑140 (MQ=255)                                                                                                                                      ccACGGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGCCg  >  2:320272/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                        TGAAGTGCATGGTCATCATGATCATGCGGGCAATCCAGAAGAAAATGATGTCGAAACCAGATACCATCACGCTGGTTGGGTGGAACTGACGCAGGGCGTCGGTATTTTCCGGCCAGCCAAGGGTAGAGAAGGTCCACAGCGCAGAAGAGAACCAGGTATCGAGAACGTCTTCGTCCTGACGCAGGACAACATCAGCACCGAGGTTATTTTCTTTACGCACTTCGTCTTCGTTGCGGCCAACATAAACGTTACCCGCTTCGTCATACCATGCCG  >  NC_000913/4482259‑4482531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑