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	90.0%	76.6 / 2.7	30	pseudogene (843/2027 nt)	SAUSA300_RS07860	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/2);  new base T (3/24);  total (4/26)
Fisher's exact test for biased strand distribution p-value = 3.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.96e-01

CTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTAC‑‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCT  >  NC_007793/1593075‑1593245                                                                                            |                                                                                    ctctTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTAC‑‑t‑ttt‑tttcc                                                                         >  1:6650584/1‑97 (MQ=255)      ccAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCAtttt                                                                     >  1:1430291/1‑100 (MQ=255)       gatctcGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCAttttt                                                                    <  1:146767/95‑1 (MQ=255)         gAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCACCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTaa                                                                  >  1:2621781/1‑100 (MQ=255)                tcttccgaTCTCCTGTACAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGt                                                           <  1:3602941/93‑1 (MQ=255)                tcttccgaTCTCCTGGCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGt                                                           <  1:3479266/93‑1 (MQ=255)                tcttccgaTCTCCTGCTCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTTCATTTTTAATTTCTGt                                                           <  1:427904/93‑1 (MQ=255)                tcttccgaTCTCCTGACCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGt                                                           <  1:2162007/93‑1 (MQ=255)                 cttccgaTCTCCTGTGCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTa                                                          <  1:2934500/94‑1 (MQ=255)                 cttccgaTCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTAC‑‑TCTTT‑TTCCATTTTTAATTTCTGTa                                                          <  1:3147946/94‑1 (MQ=255)                 aaTCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACTTT‑TTT‑TTCCATTTTTAATTTCTGt                                                           <  1:3777586/100‑1 (MQ=255)                  ccgatctattcTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTAt                                                         <  1:5430459/90‑1 (MQ=255)                   tccgaTCTCTAGTGCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATc                                                        <  1:4717293/96‑1 (MQ=255)                                                 ttCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTAc                          <  1:508832/100‑1 (MQ=255)                                                 ttCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTAc                          <  1:1093529/100‑1 (MQ=255)                                                  tCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACa                         <  1:6590326/100‑1 (MQ=255)                                                    gCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGt                       <  1:853615/100‑1 (MQ=255)                                                    gCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTACT‑‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTa                      >  1:722546/1‑100 (MQ=255)                                                              gatctatattatgttaATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTCTGATTAGTGGTACAGTATCGTAtgcc             <  1:563049/92‑3 (MQ=255)                                                              atCTAGTGCTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGACTAGTGGTACAGTATCGTAtgtg             <  1:5733116/100‑1 (MQ=255)                                                              atCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTGCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAtgtg             <  1:5013729/100‑1 (MQ=255)                                                               tCTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAtgtgg            <  1:2085197/100‑2 (MQ=255)                                                               tCTAATGTAATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTAtgtgg            <  1:2707928/100‑2 (MQ=255)                                                                tcttcgttatgttaATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt           <  1:3639681/95‑1 (MQ=255)                                                                ctgggtttatgttaATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt           <  1:1629631/94‑1 (MQ=255)                                                                cTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATgtgtg           <  1:5820493/100‑2 (MQ=255)                                                                cTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt           <  1:3465629/100‑1 (MQ=255)                                                                cTAATGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt           <  1:1588376/100‑1 (MQ=255)                                                                cTAATCTTATGTTAATAGTCTTTTTTAC‑‑T‑TTTCTTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGtt           <  1:5688006/100‑1 (MQ=255)                                                                  aaTGTTATGTTAATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTAt         >  1:2377075/1‑100 (MQ=255)                                                                         tgttaATAGTCTTTTTTACT‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCt  <  1:2585805/100‑1 (MQ=255)                                                                                            |                                                                                    CTCTTCCAGAACGTGCAATCGAATCTCCTGTCCAAACATTTATTGGAATTCGCCCATCCATATCTAATGTTATGTTAATAGTCTTTTTTAC‑‑T‑TTT‑TTCCATTTTTAATTTCTGTATCTTTTACCGACTTTATTTTGATTAGTGGTACAGTATCGTATGTGTTATCTTTTCT  >  NC_007793/1593075‑1593245

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑