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%	75.0 / NA	20	pseudogene (198/373 nt)	SAUSA300_RS04780	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (1/19);  total (1/19)

TTACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTTAAATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAAC  >  NC_007793/973635‑973798                                                                           |                                                                                          tccgatctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGc                                                                 <  1:5289563/95‑1 (MQ=255)   tccTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCaa                                                               <  1:4571551/99‑2 (MQ=255)     cttttGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCa                                                             <  1:642421/97‑1 (MQ=255)     ctctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCa                                                             <  1:4146630/100‑1 (MQ=255)      tctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCac                                                            <  1:1132363/100‑2 (MQ=255)          gtgGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAAt                                                        >  1:2014784/1‑100 (MQ=255)               ttGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCcta                                                   <  1:5533922/100‑2 (MQ=255)                 gAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCcttct                                                 <  1:2580433/100‑1 (MQ=255)                      aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCTCATCAAAAATGCCTTCTTGTAc                                            <  1:1979482/100‑1 (MQ=255)                      aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                            <  1:402926/100‑1 (MQ=255)                       tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACa                                           <  1:4276759/100‑1 (MQ=255)                        ggATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTggggtc                                          <  1:5588515/100‑6 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt                       <  1:1567589/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt                       <  1:704152/100‑1 (MQ=255)                                           tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt                       <  1:471816/100‑1 (MQ=255)                                            cttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCtg                      <  1:5474649/100‑2 (MQ=255)                                            cttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCta                      <  1:5429596/100‑1 (MQ=255)                                            cttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCta                      <  1:3169058/100‑1 (MQ=255)                                                               aTTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATgggt   <  1:708013/100‑4 (MQ=255)                                                                tttGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAAc  <  1:4008131/100‑1 (MQ=255)                                                                           |                                                                                          TTACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTTAAATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAAC  >  NC_007793/973635‑973798

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑