Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,296,380	1	.	C	91.3%	48.3 / 0.2	23	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base C (9/12);  total (9/14)
Fisher's exact test for biased strand distribution p-value = 5.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01
*	NC_000913	4,296,380	2	.	G	91.3%	46.5 / 0.4	23	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base G (9/12);  total (9/14)
Fisher's exact test for biased strand distribution p-value = 5.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑A‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTG  >  NC_000913/4296301‑4296510                                                                                     ||                                                                                                                                   ttAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAAcc                                                                       >  2:25892/1‑143 (MQ=2)   gaCGCGTGTTATCAGGCCTTCGCCAGACAGCGCCGCAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGt                                                                     <  2:466640/142‑1 (MQ=11)     tgcgTCTTTTCTTGCCTTCGCCGGCGAGCGCCGTGGTCTGCTTTTGCGTGTTTTTGTTGGTCGTACACGGCGTTCTT‑‑G‑‑CGGTATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                                   <  2:270624/142‑1 (MQ=9)     cgcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                                   <  2:185107/143‑1 (MQ=255)     cgcgTCTTATCAGGCCTACGCCAGAAAGTGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                                   <  1:523300/143‑1 (MQ=11)     cgcgTCCGATCAGGCCTACGCCAGCCAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                                   <  1:119426/143‑1 (MQ=11)          cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGCTTTCGCTCGGTTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa                                                              <  1:307629/143‑1 (MQ=11)           ttATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACTGTTGGTTAAt                                                             >  2:20841/1‑143 (MQ=255)           ttATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGCCCTATCTTAACCGTTGTTTCAt                                                             >  2:57606/1‑143 (MQ=11)                    cTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGCCGTATAAGGGCTATCCTACCCGTTGGTTAATTTTGCAAAc                                                    >  2:294311/1‑143 (MQ=14)                     tACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTACTTTTTCAACct                                                   >  1:584793/1‑143 (MQ=14)                      aCGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAActc                                                  <  1:23608/143‑1 (MQ=255)                         ccAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTc                                               <  1:240518/143‑1 (MQ=255)                          cAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTca                                              <  1:643529/143‑1 (MQ=255)                                          cTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCCCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACGCTTCACACCGCGTGTCAAAcc                              >  1:515587/1‑143 (MQ=17)                                           tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCGCACCCGGTATCGAGccc                             >  2:24181/1‑143 (MQ=18)                                               ttAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc                         <  2:238908/143‑1 (MQ=255)                                                tAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCa                        <  1:62496/143‑1 (MQ=255)                                                  gCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa                      <  1:638505/143‑1 (MQ=255)                                                   ctgcaTTTTGTAGGTCGGATAAGGCGT‑‑TTCCG‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATAc                     <  2:193974/139‑1 (MQ=21)                                                         tttGTAGGTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCa               <  1:357358/143‑1 (MQ=255)                                                                gTCGGATAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCCGGCCTATCTTAACCGCTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTCCCCTACACCCCATCTTCaa        >  1:571645/1‑143 (MQ=21)                                                                      tAAGGCGT‑‑TT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTg  >  1:108030/1‑143 (MQ=255)                                                                                     ||                                                                                                                                   TTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑‑TT‑‑A‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTG  >  NC_000913/4296301‑4296510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑