Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	2,613,256	(T)7→8	pseudogene (377/785 nt)	SAUSA300_RS13455 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,613,249	1	.	T	97.0%	86.7 / ‑4.7	33	pseudogene (384/785 nt)	SAUSA300_RS13455	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  major base T (5/27);  minor base C (0/1);  total (5/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01

TTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATA‑‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGAT  >  NC_007793/2613170‑2613341                                                                                 |                                                                                               cttccgaTCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTg                                                                           <  1:2406990/94‑1 (MQ=25)                            tCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTAtta                                                <  1:322722/100‑2 (MQ=255)                                gTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGt                                            >  1:4728000/1‑100 (MQ=255)                                 tcttggCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTg                                           <  1:3887407/96‑1 (MQ=255)                                 actaGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTg                                           >  1:4543995/3‑100 (MQ=255)                                 aataGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTg                                           >  1:3924455/2‑100 (MQ=255)                                                       cGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttg                     <  1:2624655/100‑1 (MQ=255)                                                       cGATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttg                     <  1:1268358/100‑1 (MQ=255)                                                        gATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                    <  1:1768961/100‑1 (MQ=255)                                                        gATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                    <  1:5406069/100‑1 (MQ=255)                                                        gATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                    <  1:3374268/100‑1 (MQ=255)                                                        gATTATTTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                    <  1:5588100/100‑1 (MQ=255)                                                        gATTATTTTCCATCCTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                    <  1:4807942/100‑1 (MQ=255)                                                         attattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgtt                   <  1:4300470/100‑1 (MQ=255)                                                         attattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgtg                   <  1:546858/100‑2 (MQ=255)                                                         attattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgta                   <  1:4173118/100‑2 (MQ=255)                                                          ttattTTCCATCTTGACAGGATAC‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTc                  <  1:5501263/100‑1 (MQ=255)                                                           tattTTCCATCTTGGCAGGATATTTTTTTTTTTTTTACTACGTGAATATCCTTTACTATCCTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgtg                   <  1:4790592/100‑2 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGGCAATAAAATTACCCTTCGTTGTTCt                 <  1:3638735/100‑1 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:5888052/100‑1 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:5918313/100‑1 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:4441292/100‑1 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:5323793/100‑1 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:5290996/100‑1 (MQ=255)                                                           tattTTCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:3002491/100‑1 (MQ=255)                                                           ctcttccgaTCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                 <  1:4620084/92‑1 (MQ=37)                                                              tttCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGt              <  1:401036/100‑1 (MQ=255)                                                               ttCCATCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTa             <  1:6236046/100‑1 (MQ=255)                                                                   aTCTTGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGGCAATAAAATTACCCTTCGTTGTTCTAGTATTGc         <  1:474145/100‑1 (MQ=255)                                                                       tGACAGGATAT‑‑TTTTTTTCTTTACTACGTGAACATCCTTTACTGTCATCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGaca     >  1:2910329/1‑98 (MQ=37)                                                                       tGACAGGATAT‑‑TTTTTTTCTCTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGAtt     >  1:2033303/1‑100 (MQ=255)                                                                        gACATGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTg    <  1:3245464/100‑1 (MQ=255)                                                                          cAGGATAT‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGat  <  1:486320/100‑1 (MQ=255)                                                                                 |                                                                                               TTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATA‑‑‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGAT  >  NC_007793/2613170‑2613341

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑