Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,631,153	G→A	A48V (GCA→GTA)	SAUSA300_RS08060 ←	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,631,153	0	G	A	100.0%	151.8 / NA	53	A48V (GCA→GTA)	SAUSA300_RS08060	integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (1/52);  total (1/52)

CATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTGCATTTTCAATAGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTCTTCAAATAGAGCAAACT  >  NC_007793/1631061‑1631249                                                                                             |                                                                                                 taTTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTc                                                                                           <  1:843578/99‑1 (MQ=255)      aTTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAAtgg                                                                                      <  1:5179810/100‑3 (MQ=255)          gTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAAcc                                                                                  <  1:586087/100‑1 (MQ=255)           tttAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCa                                                                                 <  1:1140632/100‑1 (MQ=255)           tttAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCa                                                                                 <  1:5701408/100‑1 (MQ=255)            ttAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCaa                                                                                <  1:3458214/100‑2 (MQ=255)            ttAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCAc                                                                                <  1:2479/100‑1 (MQ=255)            ttAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCAc                                                                                <  1:2862528/100‑1 (MQ=255)               aCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGtt                                                                             <  1:1926765/100‑1 (MQ=255)               aCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGtt                                                                             <  1:448213/100‑1 (MQ=255)               aCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGtt                                                                             <  1:1159019/100‑1 (MQ=255)                cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:1529065/100‑1 (MQ=255)                cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:1858131/100‑1 (MQ=255)                cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCCTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:4516019/100‑1 (MQ=255)                cAGCTTCATCTAATGAATTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:1586174/100‑1 (MQ=255)                  gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:4283190/100‑1 (MQ=255)                  gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:5071034/100‑1 (MQ=255)                  gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGag                                                                          <  1:3411423/100‑2 (MQ=255)                    ttCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGatat                                                                        <  1:1355040/100‑1 (MQ=255)                      cATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATgg                                                                      <  1:5490358/100‑1 (MQ=255)                      cATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATgg                                                                      <  1:3404845/100‑1 (MQ=255)                      cATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATgg                                                                      <  1:5562118/100‑1 (MQ=255)                        tCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATgggc                                                                    <  1:1835946/100‑3 (MQ=255)                         cTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACa                                                                   <  1:110868/100‑1 (MQ=255)                             tGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACATTGATATGGACAActc                                                               <  1:5777445/100‑3 (MQ=255)                               aCTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCaa                                                             <  1:3023114/100‑1 (MQ=255)                                cTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCaat                                                            <  1:2954618/100‑2 (MQ=255)                                    tgtgTTATATTTGCAAAATCCGTACCTTTAGGAAAATACTGTC‑TAAAAGGCCATTTACAGTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACt                                                       <  1:1872366/100‑1 (MQ=255)                                     gtgtTATATTTGCAAAATCCGTACCTGTATGATAATACTTTTTTAAAAGTCCATTTACATTTTCAATGGATCCCCCTTCATATGGACACCCCAACTccca                                                       <  1:2630772/100‑4 (MQ=255)                                      tgtTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAAAGGAACCGCGTTGATATGGACAACCCAAATCACTa                                                      <  1:944704/100‑1 (MQ=255)                                       tttATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTaa                                                     >  1:4548746/2‑100 (MQ=255)                                        ttATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTaaa                                                    <  1:2321152/100‑1 (MQ=255)                                              ttGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAaaataaat                                              <  1:2391073/100‑1 (MQ=255)                                                 cAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtact                                           <  1:3226042/100‑1 (MQ=255)                                                    gaTCTGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAca                                        <  1:3095588/99‑1 (MQ=255)                                                    aaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAca                                        <  1:2836796/100‑1 (MQ=255)                                                       ccGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAcaagc                                     <  1:3035856/100‑3 (MQ=255)                                                         gTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAcaattca                                   <  1:3705724/100‑1 (MQ=255)                                                                   gATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAGTACTACAATTCAATTCAtcttg                         <  1:434843/100‑2 (MQ=255)                                                                      aataCTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTAt                      <  1:3039/100‑1 (MQ=255)                                                                      aataCTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTAt                      <  1:2839341/100‑1 (MQ=255)                                                                          cTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTAtttgt                  <  1:1600839/100‑3 (MQ=255)                                                                            ttCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:1498882/99‑1 (MQ=255)                                                                            gTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:4825157/100‑1 (MQ=255)                                                                            gTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:461879/100‑1 (MQ=255)                                                                            gTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:2982906/100‑1 (MQ=255)                                                                            gTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:39865/100‑1 (MQ=255)                                                                             tCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttct               <  1:418723/100‑2 (MQ=255)                                                                             tCTTAAAAGTCCATTTACATTTACAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCa               <  1:3705010/100‑1 (MQ=255)                                                                                        cATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGcgat    <  1:4478562/100‑4 (MQ=255)                                                                                         aTTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGcgagc   <  1:391602/100‑5 (MQ=255)                                                                                          tttACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACt  <  1:4566601/100‑1 (MQ=255)                                                                                          tttACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACt  <  1:2214993/100‑1 (MQ=255)                                                                                             |                                                                                                 CATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTGCATTTTCAATAGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTCTTCAAATAGAGCAAACT  >  NC_007793/1631061‑1631249

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: ‑