Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,173,361	0	C	.	94.4%	72.4 / ‑0.7	18	pseudogene (2/442 nt)	gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base . (8/9);  total (8/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01
*	NC_000913	2,173,362	0	C	.	94.4%	69.0 / ‑1.1	18	pseudogene (1/442 nt)	gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base . (8/9);  minor base T (0/1);  total (8/10)
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

GATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGC  >  NC_000913/2173295‑2173419                                                                   ||                                                          gATTACCCGGCACAGATACAGCAATTAAAATGGTGAGTGGGATAAATATCAGGCTTGCCGATacctcc                                                           <  1:372111/68‑1 (MQ=255)  aTTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGAAAAAAATCAGGATTGCCGATaccaccg                                                          >  1:99701/1‑67 (MQ=255)          gCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGt                                                >  1:12069/1‑68 (MQ=255)            acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTcc                                              >  1:400282/1‑68 (MQ=255)                    aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAgcagca                                      >  2:142224/1‑68 (MQ=255)                      cAATTAATATGGTGAGTGGGTTAAAAATCAGGCTTGCCGATAC‑‑CTCCGCCGTATGTCCCAGCAGCAAc                                    <  2:895767/68‑1 (MQ=255)                        aTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGc                                  <  1:128232/68‑1 (MQ=255)                          tAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCg                                >  2:866694/1‑68 (MQ=255)                            aaaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGTAGCAACGCCGGa                              <  1:375790/68‑1 (MQ=255)                            aaaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGa                              <  1:399657/68‑1 (MQ=255)                               tGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGAAGCAACGCCGGATCa                           >  1:44545/1‑68 (MQ=255)                                 gTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg                         <  2:135229/68‑1 (MQ=255)                                  agAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCAGTATGTCCCCGCAGAAAAGCCGGATCAAgg                        >  1:1039014/2‑68 (MQ=255)                                       gggATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCATCAGCAACGCCGGATCAAGGCCAAt                   <  1:35608/68‑1 (MQ=255)                                       gggATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAAt                   <  1:326076/68‑1 (MQ=255)                                          aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATcgg                >  2:261026/1‑66 (MQ=255)                                               aaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACt           <  1:1227112/68‑1 (MQ=255)                                               aaTCAGGCTTGCCGATACCA‑‑CCGCCGAATGTCCCAGCAGCAACGCAGGATAAAGGACAATAAGGaaat           >  2:1185415/1‑66 (MQ=255)                                                        tGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgc  <  1:578009/68‑1 (MQ=255)                                                        tGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgc  <  2:401799/68‑1 (MQ=255)                                                                   ||                                                          GATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGC  >  NC_000913/2173295‑2173419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑