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%	54.5 / 0.8	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 (10/11);  total (10/13)
Fisher's exact test for biased strand distribution p-value = 4.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913	4,296,380	2	.	G	91.3%	57.6 / 0.7	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 (10/11);  total (10/13)
Fisher's exact test for biased strand distribution p-value = 4.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑C‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAG  >  NC_000913/4296316‑4296513                                                                  ||                                                                                                                                         aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAtttttg                                                           >  2:704902/1‑142 (MQ=255)  ggCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCa                                                          <  1:219934/143‑1 (MQ=255)  ggCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCa                                                          <  1:88438/143‑1 (MQ=255)        cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑CGC‑CCCCCACGACATCAATGCCTGCTGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAActct                                                    <  1:165320/143‑1 (MQ=17)         gCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt                                                   <  1:285536/143‑1 (MQ=255)          ccAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTc                                                  <  1:214329/143‑1 (MQ=255)              aCAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCacac                                              >  2:463494/1‑143 (MQ=255)                   gcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCACGCCTATCTTAACCGTCGGTTAATTTTTCAAACTCTTCCCACCCgct                                         >  2:325751/1‑141 (MQ=17)                     aaTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGtct                                       >  2:266939/1‑141 (MQ=255)                          ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTCACCGTTGGTTAGTTTTTCACGCTCTTCACACCCGGTAttgaac                                  >  1:88723/1‑138 (MQ=17)                          acTGATTTAGCCGTATTTTTCAGGGCGGATAAGGCTCTTA‑‑CGCGGCATC‑CGACATCTATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAAc                                  <  2:217513/142‑1 (MQ=18)                                   gCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa                         <  1:557255/143‑1 (MQ=255)                                   gCGTGATATTGTAGGTCGGATAAGGCGTGTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCGTCACACCCGGTATCAAACCCTTCCATa                         <  2:72241/143‑1 (MQ=21)                                     gTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTGTCAGGCCTGTCTTAACCGTTGGTTAATTTTTCAAACTCTTCCCACACGGTAGCAAAGCCTtacataca                       >  2:82344/1‑143 (MQ=18)                                      tGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAATCGTTGGTTAATTTTTCAAACTATTCACACCAGGCATCAAACACTCCCATACAg                      >  2:96489/1‑143 (MQ=18)                                      tGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCCCACCCGGTATCAAACCCTTCCCTACAg                      >  1:599020/1‑143 (MQ=21)                                                ggacGGATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCa            <  1:97857/140‑1 (MQ=255)                                                    ggATAAGGCGTTTACGC‑C‑GCATC‑CGACATCCATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCCCACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCa        <  2:182536/143‑1 (MQ=25)                                                    ggATAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTACTTTTTCACTCTCTTCTCACCCGTTACAAAACCAATCCATAAAACTCCAGTTCAACCa        >  1:458246/1‑143 (MQ=17)                                                       tAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTg     <  2:288347/143‑1 (MQ=255)                                                       tAAGGCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTg     <  1:541661/143‑1 (MQ=255)                                                        aaGGCGTTTACGC‑C‑GCATC‑GGACATCAATGCCTGGTGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGc    <  2:629960/143‑1 (MQ=37)                                                          ggCGTTTACGC‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACACGGAATCAAAACCTTCCATACAGCTCAGAGTAAACCAGTGCAg  >  1:591736/1‑143 (MQ=25)                                                                  ||                                                                                                                                         AGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑C‑C‑GCATC‑CGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAG  >  NC_000913/4296316‑4296513

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑