Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,631,368	C→T	intergenic (‑73/+91)	SAUSA300_RS08060 ← / ← SAUSA300_RS08065	integrase/integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,631,368	0	C	T	97.1%	184.0 / ‑4.1	69	intergenic (‑73/+91)	SAUSA300_RS08060/SAUSA300_RS08065	integrase/integrase
Reads supporting (aligned to +/- strand):  ref base C (0/2);  new base T (4/63);  total (4/65)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACTTTTGGGTAATAATGGTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTCTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAATTCTTCACGATTATTAATA  >  NC_007793/1631271‑1631464                                                                                                  |                                                                                                 tgcTTTTTGGTAATAATGGTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGtttt                                                                                                <  1:2058392/98‑1 (MQ=255)        tggTAATAATGGTTTCATAATATTTATAATCTCATTACAAACGACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCa                                                                                         <  1:5457166/99‑1 (MQ=255)         ggTAATAATGGTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGTATATAAATATCTTGTTTTTCTTTCaa                                                                                        <  1:1240642/100‑1 (MQ=255)                 tGGTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGtt                                                                                <  1:1348620/100‑1 (MQ=255)                  ggTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTa                                                                               <  1:840278/100‑1 (MQ=255)                  ggTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTa                                                                               <  1:1502127/100‑1 (MQ=255)                     ttCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACa                                                                            <  1:3105224/100‑1 (MQ=255)                         taataTTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCa                                                                        <  1:2710247/100‑1 (MQ=255)                                     tctcATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATgg                                                            <  1:12313/100‑1 (MQ=255)                                       tcATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTc                                                          <  1:4326609/100‑1 (MQ=255)                                        cATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCt                                                         >  1:5218512/1‑100 (MQ=255)                                        cATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCt                                                         <  1:3133118/100‑1 (MQ=255)                                        cATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCt                                                         <  1:2142615/100‑1 (MQ=255)                                         aTTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCtg                                                        <  1:839172/100‑2 (MQ=255)                                         aTTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTa                                                        <  1:1633252/100‑1 (MQ=255)                                         aTTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTa                                                        <  1:109880/100‑1 (MQ=255)                                         aTTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTa                                                        <  1:2183116/100‑1 (MQ=255)                                                 cTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTCCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCa                                                <  1:3078807/100‑1 (MQ=255)                                                   aCATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCaag                                              <  1:405765/100‑2 (MQ=255)                                                    ttccgatcttACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:358236/92‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:3835412/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:3921505/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:3226209/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:5366683/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:93640/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:1093691/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:1044349/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:1106825/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAAc                                             <  1:2836693/100‑1 (MQ=255)                                                    cATTGGATTTACGTGTATTAAATCTACTAGCATATAAATATCTTGTTTTTCGTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACGCTCCAAAc                                             <  1:5567943/100‑1 (MQ=255)                                                       tGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGt                                          <  1:1878433/100‑1 (MQ=255)                                                        ggATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGtg                                         <  1:3322805/100‑2 (MQ=255)                                                        ggATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTa                                         <  1:2278107/100‑1 (MQ=255)                                                          aTTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATc                                       <  1:4556252/100‑1 (MQ=255)                                                          aTTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATc                                       <  1:2956835/100‑1 (MQ=255)                                                          aTTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATc                                       <  1:5451371/100‑1 (MQ=255)                                                          aTTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATc                                       <  1:3622501/100‑1 (MQ=255)                                                          aTTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATc                                       <  1:3235557/100‑1 (MQ=255)                                                           tttACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCa                                      <  1:3375470/100‑1 (MQ=255)                                                           tttACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCa                                      <  1:2082734/100‑1 (MQ=255)                                                           tttACGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCa                                      <  1:2573511/100‑1 (MQ=255)                                                              aCGTGTATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAAtt                                   <  1:3414153/100‑1 (MQ=255)                                                                gtgtATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTc                                 <  1:1668298/100‑1 (MQ=255)                                                                  tcttccgaTCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCag                               <  1:4476848/93‑2 (MQ=255)                                                                  tcttccgaTCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCAt                               <  1:4794639/93‑1 (MQ=255)                                                                   tATTTAATCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATa                              <  1:2314835/100‑1 (MQ=255)                                                                        aaTCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTc                         <  1:1352308/100‑1 (MQ=255)                                                                         aTCTTCTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGAAATATGTTGATGGTCTAACACTCCAAACAGTATCAACTTCATAATGTcc                        <  1:3720885/100‑1 (MQ=255)                                                                         aTCTGCTAGTATATAAATATCTTGTCTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTcc                        <  1:157968/100‑1 (MQ=255)                                                                         aTCTGCTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTcc                        <  1:2733424/100‑1 (MQ=255)                                                                         aTCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTcc                        <  1:856568/100‑1 (MQ=255)                                                                         aTCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTcc                        <  1:773761/100‑1 (MQ=255)                                                                         aTCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTcc                        <  1:2972177/100‑1 (MQ=255)                                                                          tCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCa                       <  1:4776346/100‑1 (MQ=255)                                                                          tCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCa                       <  1:3251165/100‑1 (MQ=255)                                                                          tCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCa                       <  1:5388235/100‑1 (MQ=255)                                                                          tCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCa                       <  1:242527/100‑1 (MQ=255)                                                                          tCTACTAGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCa                       <  1:568959/100‑1 (MQ=255)                                                                          tCTACT‑GCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAAAAAGAAAAACAGTATCAAGGTCATAATGTCCaa                      <  1:4776520/100‑1 (MQ=255)                                                                           ctactaGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCag                      <  1:1766843/100‑2 (MQ=255)                                                                           ctactaGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCaa                      <  1:1984308/100‑1 (MQ=255)                                                                            tgctggCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCagg                     <  1:3159077/95‑3 (MQ=255)                                                                            tactaGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCaag                     <  1:749046/100‑2 (MQ=255)                                                                             actaGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAAt                    >  1:1911341/1‑100 (MQ=255)                                                                                aGCATATAAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAAttct                 >  1:5573509/1‑100 (MQ=255)                                                                                   atatAAATATCTTGTTTTTCTTTCAATAATAGTTAGCAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAATTCTTCa              <  1:4123735/100‑1 (MQ=255)                                                                                     ataAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAGATTCTTCACg            <  1:3724797/100‑1 (MQ=255)                                                                                     ataAATATCTTGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAATTCTTCACg            <  1:4025265/100‑1 (MQ=255)                                                                                     ataAATATCTTGACTATCCGTCAATAATAGTTAACAAGCAATATGTGTAAGGTCTAACACTCCAAACAGTAGCAATTGCATAATGTCCAAATTCTTCACg            <  1:763941/100‑1 (MQ=255)                                                                                               tGTTTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAATTCTTCACGATTATTAATa  >  1:5484029/1‑100 (MQ=255)                                                                                                  |                                                                                                 TACTTTTGGGTAATAATGGTTTCATAATATTTATAATCTCATTACAAACTACATTGGATTTACGTGTATTTAATCTACTAGCATATAAATATCTTGTCTTTCTTTCAATAATAGTTAACAAGCAATATGTTGATGGTCTAACACTCCAAACAGTATCAATTTCATAATGTCCAAATTCTTCACGATTATTAATA  >  NC_007793/1631271‑1631464

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: ‑