Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,428,954	T→A	pseudogene (159/189 nt)	lomR →	Rac prophage; protein LomR_1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,428,954	0	T	A	100.0%	85.2 / NA	26	pseudogene (159/189 nt)	lomR	Rac prophage; protein LomR_1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (6/20);  total (6/20)

TAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCG‑TGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACA‑CGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGA  >  NC_000913/1428882‑1429246                                                                         |                                                                                                                                                                                                                                                                                                       taatcctgcagcgtccgtcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCGGTGGG‑GTCGGTTATAAATTCTGATTAGCCNGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGGGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAACACCACGTTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATg                                                                   <  1:556687/277‑1 (MQ=255)            cgtccgtcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGt                                                        >  1:657768/13‑300 (MQ=255)                 gtcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAg                                                   <  2:434451/293‑1 (MQ=255)                  tcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCCGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCAAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGc                                                  >  1:290702/7‑300 (MQ=255)                    gttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCAt                                                <  2:217894/296‑1 (MQ=255)                         tGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTAGAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGTTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGatg                                           <  1:373905/300‑3 (MQ=255)                              ttGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCNCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGatgtggag                                      <  2:662797/300‑8 (MQ=255)                                gCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCCGAGAATCAGGATGAAGCAGGGCGTTACAGCATggctgtggagta                                    >  2:199491/1‑290 (MQ=255)                                gCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTa                                    >  1:458372/1‑300 (MQ=255)                                gCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGAAGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCAGGGCGTTAAAGCATGGATGTGGAGTa                                    >  2:359595/1‑300 (MQ=255)                                    aTGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGt                                <  1:340369/300‑1 (MQ=255)                                          gctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTTCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAc                          <  1:40836/297‑1 (MQ=255)                                          gctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAc                          <  1:34652/297‑1 (MQ=255)                                           ctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCACTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACa                         >  2:8173/3‑300 (MQ=255)                                             ccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgt                       <  1:616740/300‑2 (MQ=255)                                               tgcattGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTTTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTACACCATTCAGCTGAAAGCCAGACGTAACAGCACCAAGGAGGTGGTGGATATCG‑TGGGCTCGGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                     <  1:638999/295‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGNAAGACGGCACAGGAAAACCGGTACAGNACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                     <  2:519519/300‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                     <  1:306996/300‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTNGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                     <  1:516711/300‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGGACTGACGGATTCATTG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGTTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                     <  1:638992/300‑4 (MQ=255)                                                    tGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcc                <  1:130982/300‑9 (MQ=255)                                                      gCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGNGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctg              <  1:539376/300‑11 (MQ=255)                                                      gCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGGTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGGGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTatagtgtcatcctg              <  1:703332/300‑14 (MQ=255)                                                                  cTGACGNATTCATCG‑TTGTGGTCGGGTATAAATTTTGATTAGCCAGGTAACACANTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggt  <  2:631389/300‑23 (MQ=255)                                                                  cTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAcctgtctcttatacacatctcgcag  <  1:439326/300‑25 (MQ=255)                                                                  cTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggt  <  1:11440/300‑23 (MQ=255)                                                                         |                                                                                                                                                                                                                                                                                                       TAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCG‑TGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACA‑CGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGA  >  NC_000913/1428882‑1429246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑