Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,053,526	T→C	28.3%	R439G (AGA→GGA)	pepP ←	proline aminopeptidase P II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,053,526	0	T	C	28.3%	45.1 / 2.7	33	R439G (AGA→GGA)	pepP	proline aminopeptidase P II
Reads supporting (aligned to +/- strand):  ref base T (11/10);  new base C (3/7);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 2.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCGCAATCCGCCAGAGATTGCCAGACGCCGATGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGACCATAAACACCCAC  >  NC_000913/3053299‑3053751                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                    ttGCGCAATCCGCCAGAGATTGCCAGACGCCGATGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGAATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGCCTTAACCGGGAACTAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCCCCACCGACCATGATTACGCCCATTGCTTtct                                                                                                                                                                                                                                     >  1:95320/1‑228 (MQ=255)         tCCGCCAGAGATTGCCAGACGCCGATGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGCCTTAACCGGGAAATAGCAAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCCCCGCCGATGATTACGCTCATTGCTTTCCCccag‑ca                                                                                                                                                                                                                             >  1:314571/1‑227 (MQ=255)                     tGCCAGACGCCGATGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATCCCGCCACCGCCGATGATTACCCCCCTTGCTTTCTCGCAC‑CAccccccacccctt                                                                                                                                                                                                                >  2:658106/1‑218 (MQ=255)                                 aTGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTcc                                                                                                                                                                                                     >  1:520606/1‑227 (MQ=255)                                 aTGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCCCATTGCTTTCCCGCAA‑CAACCCTCAACGCCTCGGTTACTTCCg                                                                                                                                                                                                    >  1:282698/1‑228 (MQ=255)                                                 gACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTC‑‑CGCCCGGCCCTGCCTCCACCGCCGATGGTTCAGCCCATTCCTTT‑TCGCCGCCAACCACCAACCCTTCGATTTCTTCCGTCTGTTCCCCCACACt                                                                                                                                                                                    >  2:5883/1‑228 (MQ=255)                                                              cgccAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGCCG‑CGCCC‑GCCCTGCCCCCACCGACGATGATTCCGCCCATAGCTTTCTCTCAG‑CAACCCTCAACGCTTCCATTTATTCCCGCGTTTTCACCACGCTGACGGGGAggggc                                                                                                                                                                       >  2:373984/1‑225 (MQ=255)                                                                        aTCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCCCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGAGAGGTTTTCGTTACCg                                                                                                                                                              >  1:366675/1‑227 (MQ=255)                                                                           ctttctCCCTCAAAACCCGGGTGGAGCGTGGGACTGGGGCGCAGGCGCTTAAATCAAGTGGCCGTGCAGCCCCCC‑GTGACTGAACCGGAAAATGGCCACCG‑CCAGCCTCG‑ACCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGtt                                                                                                                                                           <  2:314571/223‑1 (MQ=255)                                                                              cGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCCCATTGCTTTCCCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCCCCACGCTGGCGGAAAGGGTTTAGTTAACGGTTTTgg                                                                                                                                                       >  2:558851/1‑228 (MQ=255)                                                                                      aaaGCCGGGAG‑GAGCCTGTGACTCGGGCGCCGTCGCTTCAATCAAATGGCCCGGCCGCCCCCC‑GTGAATTAACCGGGAAATAGCAAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATcaca                                                                                                                                              <  1:610398/228‑1 (MQ=255)                                                                                              gAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGCCGGTGAGGTTTTCTGTTCCGGTTTTGG‑TAATCACAATtttgtc                                                                                                                                      >  1:405398/1‑228 (MQ=255)                                                                                                               tGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACAACGCTGGCGGTGAGGGTTTCTTTTCCCGTTTCTG‑GAATCACACAGTTGGCTTCCATTAGAATTCCg                                                                                                                      >  1:644964/1‑228 (MQ=255)                                                                                                               tGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCACCAACGCCTCGATTTCTTCCGGCTTTTTCACCCCGCTGGCGGCGTGGTTTTCGTTTCCGGGTTCGGATACGCACAA‑GTCGGCTTCAAACCAAATGcca                                                                                                                      >  2:7477/1‑227 (MQ=255)                                                                                                                 gcggAGTCTCTTCAACAAAATG‑GCCGGGAGCCCCCCGGTGCTCTAACCGGGAAA‑AGCCCGGGCCCAGCGTCG‑GCCCC‑GCCATGCCGCCACCGGCGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGa                                                                                                                     <  2:95320/227‑1 (MQ=255)                                                                                                                 gcctgatCGCTTAAATCAATGGTCCCGGAAGCGCCCC‑GTGATTTAACGGGGAACTCCCCAGCG‑CCCGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGa                                                                                                                     <  1:364864/221‑1 (MQ=255)                                                                                                                       tCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGGGGTTTTCTTTTCCGTGTTCGG‑TACTACCAATATCGTCTTCATAACAAAAGCCggcaacccg                                                                                                              >  2:572965/1‑220 (MQ=255)                                                                                                                                    aTGTCCCGGAAGCCCCCG‑GGGACTTAACCGGAAAATGCCCAGCG‑CCAGGTGCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTgg                                                                                                  <  1:115327/227‑1 (MQ=255)                                                                                                                                                 gcCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGGTTTTCTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCCAGACCGCGATATTGTTTTTGCACTTTTTCATCCg                                                                                    >  1:418894/1‑228 (MQ=255)                                                                                                                                                  cccc‑GTGACTTAACCGGGAAATAGCCAGCG‑CCCGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCgg                                                                                   <  1:414270/228‑1 (MQ=255)                                                                                                                                                     cggTGACTGAACAGGGAATTACCCAGCG‑CCGGCGCCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGATCATTGCTTTCCCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGgcg                                                                                 <  1:19642/226‑1 (MQ=255)                                                                                                                                                                 cGGGAAATGGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGATTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGcc                                                                     <  1:104070/228‑1 (MQ=255)                                                                                                                                                                         ccgccgcg‑cccgccTCC‑CGCCC‑GCCATGCCGCCACCGCCGATGATTACGCTCATTGCTTTCGCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGctct                                                             <  1:592296/223‑1 (MQ=255)                                                                                                                                                                          gcccccg‑cccgcgTCGCCCCCC‑GCCATGCCCGCACCGATGCTGTTTACCCTCAGTGCTTTCCCGCAG‑GACCCATAAACGTTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAAGCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGctct                                                             <  2:282698/223‑1 (MQ=255)                                                                                                                                                                                            cgccc‑gccATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCCCCACGCTGGCGGTAAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGcc                                            <  1:558851/228‑1 (MQ=255)                                                                                                                                                                                             gccc‑gtcATGCCGCCACCGACGGTGATTACGCCCATTGCTTTCGCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAAGCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGcc                                            <  1:60520/227‑1 (MQ=255)                                                                                                                                                                                             cccc‑ggcATGCCGCCACCGACGATGATTACGTTTATTGCTTTCCCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATg                                              <  1:339067/224‑1 (MQ=255)                                                                                                                                                                                                                gccgttcatTACGCTAATTTCTTTCCCGCGA‑CCACCATCATCGCTTGGATTTCTTCCGGCTTATTCCCCGCGCTGGCTGGGAGGTTTTTGTTGCCGGTGTCGG‑AAATCACAATGTCGTCGTCGATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCGCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCgcgag                         <  2:578370/221‑1 (MQ=255)                                                                                                                                                                                                                        ttACGCCCATTGCTTGTCCGGCG‑CAACCATTAACGTTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTg                 <  1:5883/228‑1 (MQ=255)                                                                                                                                                                                                                         tccGCTCCTTGCTGTCCCTGAG‑CAGCCATAACCTCTTGGTTTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCCGAATTTCGTCTTCAATACTAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCGAGAATGCGCGAGCGATCCTGa                <  2:478561/226‑1 (MQ=255)                                                                                                                                                                                                                         tacggccATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTTCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGa                <  1:658106/222‑1 (MQ=255)                                                                                                                                                                                                                             cTCATTGGTTTCCCGCAG‑CAACCATCCACGCTGCGATTTCGTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGACCAt            <  1:222791/228‑1 (MQ=255)                                                                                                                                                                                                                             cTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑Taa                                                                                                                                                   >  2:525120/1‑93 (MQ=255)                                                                                                                                                                                                                              tCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAAt                                                                                                                                                  <  1:525120/93‑1 (MQ=255)                                                                                                                                                                                                                                        ctcGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGGTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCAATTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCGCCAGCCATCCTGACCATAAACACCCAc  >  1:204590/1‑227 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                    TTGCGCAATCCGCCAGAGATTGCCAGACGCCGATGCGCGCCAGTTGCTGACAGGTACCCGCCGCCAGCGCTATCGCTCGTCCATCAAAGCCCGGAT‑GAGCATGTGACTCTGGCGCAGTCGCTTCAATCAAATGTACCGGCAGCGCCCC‑GTGACTTAACCGGGAAATAGCCAGCG‑CCAGCGTCG‑CGCCC‑GCCATGCCGCCACCGACGATGATTACGCTCATTGCTTTCTCGCAG‑CAACCATCAACGCTTCGATTTCTTCCGGCTTTTTCACCACGCTGGCGGTGAGGTTTTCGTTACCGGTTTCGG‑TAATCACAATGTCGTCTTCAATACGAATGCCGATACCGCGATATTGTTCTGGCACTTCTGCATCCGGCGCAATATACAGCCCTGGCTCTACGGTCAGTACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGACCATAAACACCCAC  >  NC_000913/3053299‑3053751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑