Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	973,711	Δ1 bp	pseudogene (196/373 nt)	SAUSA300_RS04780 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	973,709	0	A	.	100.0%	87.5 / NA	23	pseudogene (198/373 nt)	SAUSA300_RS04780	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (3/20);  total (3/20)

TTACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTTAAATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATA  >  NC_007793/973635‑973781                                                                           |                                                                         cgatctctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGc                                                <  1:4658495/96‑1 (MQ=255) cgatctctTGTAGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGc                                                <  1:1481514/96‑1 (MQ=255)    gatctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATc                                             <  1:1535819/98‑1 (MQ=255)     ctctTGTCGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCa                                            <  1:558834/100‑1 (MQ=255)       ctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaaa                                          >  1:2177491/1‑100 (MQ=255)       ctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaaa                                          >  1:5425135/1‑100 (MQ=255)       ctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaaa                                          >  1:3639009/1‑100 (MQ=255)                    aaaTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGt                             <  1:2763185/100‑1 (MQ=255)                    aaaTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGt                             <  1:48443/100‑1 (MQ=255)                      aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                           <  1:14878/100‑1 (MQ=255)                      aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                           <  1:2194835/100‑1 (MQ=255)                      aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                           <  1:3004103/100‑1 (MQ=255)                      aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                           <  1:5353073/100‑1 (MQ=255)                       tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACa                          <  1:938520/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt      <  1:4715179/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt      <  1:5089806/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt      <  1:5324060/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt      <  1:3822063/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt      <  1:1951886/100‑1 (MQ=255)                                            cttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCtg     <  1:4691068/100‑2 (MQ=255)                                             ttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCtag    <  1:714052/100‑2 (MQ=255)                                               cttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAGCTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCtaata  <  1:1705754/100‑1 (MQ=255)                                               cttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCACCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGccagat  <  1:2474306/100‑6 (MQ=255)                                                                           |                                                                         TTACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTTAAATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATA  >  NC_007793/973635‑973781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑