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	94.0%	141.1 / 1.8	50	pseudogene (384/785 nt)	SAUSA300_RS13455	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base T (9/38);  total (9/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.70e-01

ATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATA‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGATAT  >  NC_007793/2613150‑2613343                                                                                                     |                                                                                               gttGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGata                                                                                                 >  1:3747760/2‑100 (MQ=255)           gAACTTAAAGTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATA‑ttttttttct                                                                                      <  1:3173488/100‑4 (MQ=255)                tAAAGTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTtact                                                                                  <  1:2239300/100‑1 (MQ=255)                ggcaGTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTtact                                                                                  >  1:4034794/4‑100 (MQ=255)                    gTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGt                                                                              <  1:732458/100‑1 (MQ=255)                        tCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAat                                                                          <  1:4332017/100‑1 (MQ=255)                               ctTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCttt                                                                   >  1:5165099/1‑100 (MQ=255)                                                ttccgatctggCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTAttt                                                  <  1:1352539/91‑1 (MQ=25)                                                     tctaGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTg                                             <  1:1030604/98‑1 (MQ=255)                                                     tataGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCCTCAGTTATTTCGGTg                                             >  1:261497/1‑100 (MQ=255)                                                      ataGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGa                                            >  1:4363872/1‑100 (MQ=255)                                                       taGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGAc                                           >  1:5505986/1‑100 (MQ=255)                                                        aGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACa                                          >  1:5664544/1‑100 (MQ=255)                                                        aGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACa                                          >  1:19905/1‑100 (MQ=255)                                                             atgttgGAATAATTCGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATaaa                                     >  1:3825370/2‑100 (MQ=255)                                                                           cGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttt                       <  1:4289656/100‑2 (MQ=255)                                                                           cGATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATCTCGGTGACAATAAAATTACCCTTCgttg                       <  1:1392775/100‑1 (MQ=255)                                                                            gATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                      <  1:1908051/100‑1 (MQ=255)                                                                            gATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                      <  1:3807826/100‑1 (MQ=255)                                                                            gATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                      <  1:3394244/100‑1 (MQ=255)                                                                            gATTATTTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgt                      <  1:5266465/100‑1 (MQ=255)                                                                            gATTATTTTCCATCTTGACAGGATA‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgta                     <  1:5030181/100‑2 (MQ=255)                                                                             attattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATAACCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgtt                     <  1:2326669/100‑1 (MQ=255)                                                                              ttattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCgttgtgg                    <  1:4494863/100‑3 (MQ=255)                                                                              ttattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTc                    <  1:1589421/100‑1 (MQ=255)                                                                              ttattTTCCATCTTGACAGGATA‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:4115326/100‑1 (MQ=255)                                                                              gctcttccgaTCTTG‑CAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:763402/91‑1 (MQ=37)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:3102896/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:1566507/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:1472437/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:5525621/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:5034817/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:615307/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:5563600/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:5032718/100‑1 (MQ=255)                                                                               tattTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGCGACAATAAAATTACCCTTCGTTGTTCt                   <  1:306577/100‑1 (MQ=255)                                                                               ctcttccgaTCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTGCCCTTCGTTGTTCt                   <  1:5571269/92‑1 (MQ=37)                                                                               ctcttccgaTCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCt                   <  1:802559/92‑1 (MQ=37)                                                                                tcttccgaTCTTGACAGGATATTTTTTTTCTTTACTACGTAAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTa                  <  1:1376599/93‑1 (MQ=38)                                                                                attTTCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTa                  <  1:2417040/100‑1 (MQ=255)                                                                                 ttttCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTat                 <  1:3289640/100‑2 (MQ=255)                                                                                 ttttCCATCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAg                 <  1:1661811/100‑1 (MQ=255)                                                                                       aTCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGc           <  1:123333/100‑1 (MQ=255)                                                                                       aTCTTGACAGGATA‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCg          <  1:4851430/100‑1 (MQ=255)                                                                                        tCTTGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGcc          <  1:5377430/100‑2 (MQ=255)                                                                                           tGACGGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGAtt       <  1:3983316/100‑1 (MQ=255)                                                                                           tGACAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGAtg       <  1:169440/100‑2 (MQ=255)                                                                                           tGACAGGATATTTTTTTTCTTTACTACGAGAATATCCTTTACTATCTTCAGTTATTTCAGTAACAATAGAATTACCCTTCGTTGATCTAgatcgtaatac       >  1:1149416/1‑90 (MQ=255)                                                                                              cAGGATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGat    <  1:3733109/100‑1 (MQ=255)                                                                                                ggATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGatat  <  1:2487982/100‑1 (MQ=255)                                                                                                ggATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGatat  <  1:2079883/100‑1 (MQ=255)                                                                                                ggATATTTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGatat  <  1:1791821/100‑1 (MQ=255)                                                                                                     |                                                                                               ATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTAACTTGTCATCCGGTATAGGCTTTGTTGGAATAATTCGATTATTTTCCATCTTGACAGGATA‑TTTTTTTCTTTACTACGTGAATATCCTTTACTATCTTCAGTTATTTCGGTGACAATAAAATTACCCTTCGTTGTTCTAGTATTGCGATTGATAT  >  NC_007793/2613150‑2613343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑