Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	895,222	0	T	C	73.3%	13.4 / 4.5	15	intergenic (‑93/‑941)	SAUSA300_RS04395/SAUSA300_RS04400	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (2/2);  new base C (2/9);  total (4/11)
Fisher's exact test for biased strand distribution p-value = 5.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.17e-01

ATTTTCTCCTATAATTTATTTGCAATCGATTACAAAGTAATTTTACAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAAGATATAAAATATTATTATTACAATATATTAATTTTGAGCTGGAAATATTCGTTATTTATGCTATAATCATTTTAGACACAGCAATGTGTTC  >  NC_007793/895133‑895310                                                                                          |                                                                                         attttCTCCTATAACTTATTTGCAATCGATTACAAAGTAATTTTAGAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAATCCATAAAAtttt                                                                                <  1:2267771/100‑1 (MQ=255)        ccTGTAACTTATTTGCAATCGATTACAAAGTAATTTTAGAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAATCCATAAAATtttatcattg                                                                         >  1:1184594/1‑99 (MQ=255)        ccTATAATTTATTTGCAATCGATTACAAAGTAATTTTACAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAAGATATAAAATAttattatta                                                                         >  1:3067669/1‑100 (MQ=255)        ccTATAATTTATTTGCAATCGATTACAAAGTAATTTTACAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAAGATATAAAATAttattatta                                                                         >  1:3859474/1‑100 (MQ=255)                               tACAAAGTAATTTTACAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAAGATATAAAATATTATTATTACAATATATTAATTTTGAGCTggg                                                  <  1:6202637/100‑2 (MQ=255)                                aCAAAGTAATTTTAGAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGaa                                                 >  1:4361186/1‑100 (MQ=255)                                         ttttATAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAAGATATAAAATATTATTATTACAATATATTAATTTTGAGCTGGAAATATTCGtt                                        <  1:2924713/100‑1 (MQ=255)                                            tagagttattattTATGTAAATCAATTAAATAATTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGtcatt                                     <  1:4394826/95‑1 (MQ=255)                                             agaaTTATTATTTATGTAAATCAATTAAATAATTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGtcattt                                    <  1:4776130/98‑1 (MQ=255)                                                    ttatttatGTAAATCAATTAAATAATTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGTCATTTATGCtat                             <  1:564969/100‑1 (MQ=255)                                                             tAAATCAATTAAATAATTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGTCATTTATGCTATAATCGtttt                    <  1:5112944/100‑1 (MQ=255)                                                                           aatTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGTCATTTATGCTATAATCGTTTTAGACACAGCAAtgt      <  1:1682216/100‑1 (MQ=255)                                                                           aatTATTAACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGTCATTTATGCTATAATCGTTTTAGACACAGCAAtgt      <  1:5350578/100‑1 (MQ=255)                                                                               attaACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGTCATTTATGCTATAATCGTTTTAGACACAGCAAtgtgcct  <  1:5961437/100‑4 (MQ=255)                                                                               attaACAAATCCATAAAATTTTATCATTGAAATATAATAATTTTGAGCTAGAAATATTCGTCATTTATGCTATAATCGTTTTAGACACAGCAATGTGTTc  <  1:1033480/100‑1 (MQ=255)                                                                                          |                                                                                         ATTTTCTCCTATAATTTATTTGCAATCGATTACAAAGTAATTTTACAATTATTATTTATGTAAATCAATTAAATAATTATTAACAAAGATATAAAATATTATTATTACAATATATTAATTTTGAGCTGGAAATATTCGTTATTTATGCTATAATCATTTTAGACACAGCAATGTGTTC  >  NC_007793/895133‑895310

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑