Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,296,297	+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_pae_tpiA	4,296,296	1	.	C	95.2%	49.1 / NA	22	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  major base C (14/6);  minor base G (0/1);  total (14/8)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913_3_pae_tpiA	4,296,296	2	.	G	90.5%	48.0 / ‑6.6	22	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  major base G (14/5);  minor base C (0/2);  total (14/8)
Fisher's exact test for biased strand distribution p-value = 1.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑C‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGC  >  NC_000913_3_pae_tpiA/4296210‑4296430                                                                                        ||                                                                                                                                         gCGACCCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTAAGCGTGACTGTGTAGGTCGGGTAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAAc                                                                            >  1:250139/1‑149 (MQ=1)   gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCg                                                                          >  1:564709/1‑149 (MQ=9)            cgcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAt                                                                 >  2:550018/1‑149 (MQ=255)             tcttCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCATGCCTATCTTCACCGTTGGTTAAtt                                                                <  1:535856/146‑1 (MQ=11)                tCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAttttt                                                             >  2:603382/1‑149 (MQ=255)                tCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAttttt                                                             >  1:378793/1‑149 (MQ=255)                    aTCAGGCCTACGCCAGACAGCGCAATAGCCTTAGTTAGCGTGATTTTCTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAAGGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa                                                         <  1:175004/149‑1 (MQ=14)                        ggCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGCATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTGAACCGTTGGTTAATTTTTCAAActct                                                     >  2:602959/1‑149 (MQ=14)                          gcgaCGCGAGACAGCGCAATTGCCTGATTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTTACCC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTc                                                   <  2:375338/146‑1 (MQ=17)                            tACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTCGCTTAATCTTTCTAACTCTTcac                                                 >  2:104033/1‑149 (MQ=14)                                    aCAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTa                                         >  2:222738/1‑149 (MQ=255)                                              aGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCtt                               <  1:550018/149‑1 (MQ=255)                                                ccttgtttAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑CTCTGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCCTATCAGGCCTATCTTCACCGTTGGTTAATTTTTCAAACTCTCCACACCCGGTATCAAACCCTTcc                             <  1:77794/144‑1 (MQ=18)                                                 cTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCTCACCCGGCATCAAACCCTTcct                            >  2:525732/1‑148 (MQ=18)                                                   gATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa                          <  1:104033/149‑1 (MQ=255)                                                   gATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTACCAAACCCTTCCATa                          >  2:609949/1‑149 (MQ=255)                                                     tttAGCTTGATTTTGTAGGTCGGATAGTTCGTTTAGCC‑C‑GCATTCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa                        <  2:200976/149‑1 (MQ=25)                                                          cGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCa                   >  1:63116/1‑149 (MQ=255)                                                          cGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCCGTACCAAACCCTTCCATCCCGCTCa                   >  2:485284/1‑149 (MQ=18)                                                                       gTCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTg      <  1:331920/149‑1 (MQ=255)                                                                        tCGGATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGc     >  2:494764/1‑149 (MQ=255)                                                                           gATAAGGCGTTTACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTCATTTTTCAAACTCTTCACACCCCGTATCAAACCCTCCCCTACAGCTCAGGTTCAACCAGTGCAgc  >  2:96220/1‑149 (MQ=25)                                                                                        ||                                                                                                                                         GCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑C‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGC  >  NC_000913_3_pae_tpiA/4296210‑4296430

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: ‑