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	93.3%	34.8 / ‑3.4	15	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (5/9);  total (6/9)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913	4,296,380	2	.	G	93.3%	35.3 / ‑3.4	15	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (5/9);  total (6/9)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTA‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAA  >  NC_000913/4296302‑4296504                                                                                  ||                                                                                                                             tgaCGCGTCGTATCAGGCCCACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCg                                                                <  1:481155/141‑1 (MQ=11)         cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa                                                        <  1:369040/143‑1 (MQ=255)         cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa                                                        <  1:399806/143‑1 (MQ=255)               aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                  <  1:273068/143‑1 (MQ=255)               aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                  <  1:517294/143‑1 (MQ=255)               aGGCCTACGCCAGACAGCGCAATAGCCTGAGGTAGCGTGATTTTGTAGGCCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                  <  1:45462/143‑1 (MQ=14)                      cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCCTATCAGGCCTATCTTAACCGTTGGTAAATTTTCCCAActct                                           >  2:296655/1‑143 (MQ=14)                                       gCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa                          <  1:278379/143‑1 (MQ=255)                                               tAGCGTGATTTTGTAGGTCGGATAAAGCGATATAA‑‑CCGCAGCCTACATCAATGCCTGATGCGACGCTGGCGGCTGCCTAGCAGACCGAGCTTAGCTTGTGAGTAATGTTGCAAACTCTGCACACCCGGGATCAAAcgcgtcac                  >  2:132911/1‑136 (MQ=9)                                                aGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTCGGTTAATTTTTCAAACTATTCACACCCGGTATCAAACCCTACCAt                 >  2:472641/1‑143 (MQ=18)                                                  cGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATAc               <  1:474335/143‑1 (MQ=255)                                                        tttGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAACCTCTTCCCACCCGGTATCAAACCCTTCCATACAGCTCa         >  1:421975/1‑143 (MQ=21)                                                           gTAGGTCGGGTAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGt      <  2:202084/143‑1 (MQ=255)                                                               gTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTCTCAGGCCTATCTTAACCGCTGGTTAATTTTTCAAACTCTTCACACCCGGGATCAAACCCTTCCACACAGCTCAggcccaa  >  2:190061/1‑138 (MQ=21)                                                               attggATAATGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCACGTCTATCTTAACCGTTGGTTAATTTTTCAAACCCTTCACACCCGGTATCAAACCCATCCATACCGCTCACGTTCaa  >  2:78494/4‑143 (MQ=21)                                                                                  ||                                                                                                                             TAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTA‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAA  >  NC_000913/4296302‑4296504

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: ‑