Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,173,363	Δ2 bp	pseudogene (915‑916/1358 nt)	gatC ←	galactitol‑specific PTS enzyme IIC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,173,361	0	C	.	93.3%	60.9 / ‑1.1	15	pseudogene (918/1358 nt)	gatC	galactitol‑specific PTS enzyme IIC component
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base . (8/6);  total (8/7)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01
*	NC_000913	2,173,362	0	C	.	93.3%	60.2 / ‑2.2	15	pseudogene (917/1358 nt)	gatC	galactitol‑specific PTS enzyme IIC component
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base . (8/6);  total (8/7)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAA  >  NC_000913/2173297‑2173423                                                                 ||                                                              ttACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccac                                                                >  1:3235888/1‑65 (MQ=255)   aCCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccg                                                              >  1:1878385/1‑64 (MQ=255)   aCCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccg                                                              >  1:2306679/1‑64 (MQ=255)     ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgcc                                                            <  1:1308047/65‑4 (MQ=255)     ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgcc                                                            >  1:1926438/1‑62 (MQ=255)     ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgcc                                                            >  1:1177750/1‑62 (MQ=255)            acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATAC‑‑CCCCGCCGTATGTc                                                   <  1:2654884/65‑1 (MQ=255)                aCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcag                                               >  1:2019900/1‑65 (MQ=255)                  aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATCCCA‑‑CCGCCGTATGTCCcagca                                             <  1:2009675/65‑1 (MQ=255)                  aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca                                             >  1:2695841/1‑65 (MQ=255)                  aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca                                             >  1:1881349/1‑65 (MQ=255)                   gCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCGGATGCCA‑‑CCGCCGTATGTCCcagcag                                            <  1:921057/65‑1 (MQ=255)                        tAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATCCCA‑‑CCGCCGTATGTCCCAGCAGCAACg                                       <  1:3093176/65‑1 (MQ=255)                         aaaaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGc                                      <  1:697214/65‑1 (MQ=255)                             tGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGa                                  >  1:675332/1‑65 (MQ=255)                                tGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCa                               >  1:1356809/1‑65 (MQ=255)                                   gTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCACgg                            >  1:1084756/1‑65 (MQ=255)                                     gggATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGcc                          >  1:146896/1‑65 (MQ=255)                                        aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAAt                       <  1:1508450/65‑1 (MQ=255)                                          aaaaaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCa                     >  1:432408/1‑65 (MQ=255)                                             caTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGa                  <  1:2635771/64‑1 (MQ=255)                                                cAGGCTTGCCGATCCCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACt               <  1:983925/65‑1 (MQ=255)                                                cAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACt               <  1:591651/65‑1 (MQ=255)                                                  ggCTTGCCGATTCCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTcc             <  1:1965363/65‑1 (MQ=255)                                                   gCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCt            >  1:2289589/1‑65 (MQ=255)                                                   gCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCt            >  1:120785/1‑65 (MQ=255)                                                               acccccGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGaa  <  1:1164761/63‑1 (MQ=255)                                                                 ||                                                              TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAA  >  NC_000913/2173297‑2173423

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑