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%	145.3 / NA	38	pseudogene (198/373 nt)	SAUSA300_RS04780	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (0/38);  total (0/38)

TTTTACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTTAAATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAACATA  >  NC_007793/973633‑973801                                                                             |                                                                                             cttccgatctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTc                                                                      <  1:3928098/93‑1 (MQ=255)  ttccgatctTGTGGCTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTct                                                                     <  1:2040550/94‑2 (MQ=255)   tccgatctTGGTGGTTGAAAAATGGATCAACAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGc                                                                    <  1:1171384/95‑1 (MQ=255)   ctACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGc                                                                    <  1:2375201/99‑1 (MQ=255)   cgatctctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGc                                                                    <  1:3752149/96‑1 (MQ=255)     atctctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCAt                                                                  <  1:5480706/98‑1 (MQ=255)       cttttGTGGGTTGAAAAATGGAGCATCAGAGATAGACTTCTTCTTTGTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCa                                                                <  1:2719380/97‑1 (MQ=255)       ctctTGTAGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCa                                                                <  1:5599081/100‑1 (MQ=255)       ctctTGTAGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCa                                                                <  1:4477349/100‑1 (MQ=255)        tctcgcggtttGAAAAATGGATCATCAGATATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaa                                                               <  1:4860135/91‑1 (MQ=255)        tctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaa                                                               <  1:570720/100‑1 (MQ=255)        tctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaa                                                               <  1:1313763/100‑1 (MQ=255)         ctTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCaaa                                                              <  1:1251449/100‑1 (MQ=255)               ggTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGca                                                        <  1:2249948/100‑2 (MQ=255)                 ttGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCctt                                                      <  1:4425449/100‑1 (MQ=255)                    aaaaaTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCcttccc                                                   <  1:3723069/100‑3 (MQ=255)                      aaaTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTga                                                 <  1:2781873/100‑2 (MQ=255)                       aaTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGtt                                                <  1:1022152/100‑2 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:3109060/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:140324/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:386884/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:3930542/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:3934219/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:4411969/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:5346652/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:5142962/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:2203611/100‑1 (MQ=255)                        aTGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAc                                               <  1:5031393/100‑1 (MQ=255)                         tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTAcc                                              <  1:3938748/100‑2 (MQ=255)                         tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACa                                              <  1:1075977/100‑1 (MQ=255)                         tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACa                                              <  1:1599254/100‑1 (MQ=255)                         tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACa                                              <  1:5009225/100‑1 (MQ=255)                         tGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACa                                              <  1:360302/100‑1 (MQ=255)                          ggATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAGCCATAACTTGTCGCATCAAAAATGCCTTCTTGTACat                                             <  1:4965454/100‑2 (MQ=255)                                             tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt                          <  1:2960203/100‑1 (MQ=255)                                             tcttcttTTTCGAAGATGACATTTGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCt                          <  1:3009236/100‑1 (MQ=255)                                                                    tGATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAACAt   <  1:2543530/100‑1 (MQ=255)                                                                     gATACTTT‑AATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAACATa  <  1:2683624/100‑1 (MQ=255)                                                                             |                                                                                             TTTTACCTCTTGTGGGTTGAAAAATGGATCATCAGAGATAGACTTCTTCTTTTTCGAAGATGACATTTGATACTTTAAATCTTCTAAAACCATAACTTGTCGCATCAAAAATGCCTTCTTGTACAAGTAAAATCAAAAATATGCTAATAAAAATAATTAATGAAACATA  >  NC_007793/973633‑973801

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: ‑