Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	4,296,363	+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_3_hsa_tpiA	4,296,362	1	.	C	96.2%	76.5 / ‑3.5	26	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (7/18);  total (7/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913_3_hsa_tpiA	4,296,362	2	.	G	96.2%	74.0 / ‑3.6	26	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (7/18);  total (7/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTA‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTT  >  NC_000913_3_hsa_tpiA/4296281‑4296483                                                                                     ||                                                                                                                          gCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCCATAGCCTGATTTTGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                          <  1:15163/149‑1 (MQ=11) gCTAAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                          <  1:16013/149‑1 (MQ=255)    tAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGtt                                                       <  1:276594/149‑1 (MQ=255)    tAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGtt                                                       >  1:316390/1‑149 (MQ=255)        gcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAtt                                                   >  2:337810/1‑149 (MQ=255)          gTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAtttt                                                 <  1:61151/149‑1 (MQ=255)             ttATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCa                                              <  1:460576/149‑1 (MQ=255)               aTCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa                                            <  1:162578/149‑1 (MQ=255)                  aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAActc                                         <  2:474125/149‑1 (MQ=255)                  aGGACTGCGCCGGAGAGCGCAGTGGTCTAATTTAGCGGTTTTTTGTTGGTCGTATACGGCGTTTTTG‑‑CGGTCTCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAActc                                         <  2:330365/149‑1 (MQ=12)                    gCCTACGCCAGACAGCGCAATAGCTTGCTGTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt                                       <  1:496388/149‑1 (MQ=17)                          gCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc                                 <  1:503359/149‑1 (MQ=255)                            cAGACAGCGACATAGCCTGACTTAGCGTGATTTTTTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCg                               <  2:39378/149‑1 (MQ=17)                               aCAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTa                            <  1:337810/149‑1 (MQ=255)                                 aGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCCTCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATc                          <  1:202245/149‑1 (MQ=255)                                           ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc                >  1:563820/1‑149 (MQ=255)                                           ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc                <  1:349101/149‑1 (MQ=255)                                           ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGGCTTATCAGGCCTATCTTAACCGTTGGTTTATTTTTCAAACTCTTCACACCCGGTTTCAACCCCTTcc                >  1:316010/1‑149 (MQ=18)                                                tttAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa           <  2:316390/149‑1 (MQ=255)                                                     cGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa           >  1:595343/1‑144 (MQ=255)                                                     cGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa           <  2:595343/144‑1 (MQ=255)                                                      gTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAg     <  1:11627/149‑1 (MQ=255)                                                      gTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGGCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTCCACCCCCGGTCTCAACCCCTTCCACACAGCTccg     >  2:278404/1‑147 (MQ=18)                                                       tGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAgg    <  2:440984/149‑1 (MQ=255)                                                       atgatttGTAGGCCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAgg    >  2:520522/5‑149 (MQ=25)                                                         aTTTTGTAGGTCGGATAAGGCG‑‑TTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGtt  <  1:4243/149‑1 (MQ=255)                                                                                     ||                                                                                                                          GCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTA‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTT  >  NC_000913_3_hsa_tpiA/4296281‑4296483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑