Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,593,171	(T)6→7	pseudogene (837/2027 nt)	SAUSA300_RS07860 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,593,165	1	.	T	94.1%	44.8 / ‑3.3	17	pseudogene (843/2027 nt)	SAUSA300_RS07860	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (5/11);  total (5/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

CCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑AC‑TTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTT  >  NC_007793/1593080‑1593249                                                                                        |                                                                                     ccAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCAtttt                                                                         >  1:5694506/1‑100 (MQ=255)         tGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCt                                                                 >  1:2388844/1‑100 (MQ=255)               cttccgatcTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTGTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCt                                                           <  1:5793128/92‑1 (MQ=255)                      ccTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCg                                                    >  1:2562393/1‑100 (MQ=255)                      ccTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCg                                                    >  1:5737172/1‑100 (MQ=255)                                            ttCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTAc                              <  1:2416322/100‑1 (MQ=255)                                               gCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGt                           <  1:4790077/100‑1 (MQ=255)                                                  gatccatATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATc                        >  1:4187949/2‑100 (MQ=255)                                                    tccatATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGt                      <  1:702173/100‑1 (MQ=255)                                                      catATCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTag                    <  1:3871961/100‑2 (MQ=255)                                                        tatCTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAtgt                  <  1:3811354/100‑1 (MQ=255)                                                           cttgtgttatgttaATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt               <  1:3132512/96‑1 (MQ=255)                                                           cTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt               <  1:462452/100‑1 (MQ=255)                                                           cTAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt               <  1:3715776/100‑1 (MQ=255)                                                            tAATGTTATGTTAATAGTCTTTTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTa              <  1:2316249/100‑1 (MQ=255)                                                              atgttatgttAATAGTCTATTTT‑ACTTTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTaagagcgtcg            <  1:2383673/100‑10 (MQ=255)                                                                        aaTAGTCTTTTTTAAT‑TTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTAttt  <  1:4425679/100‑1 (MQ=255)                                                                                        |                                                                                     CCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTT‑AC‑TTTTTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCTATTT  >  NC_007793/1593080‑1593249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑