Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	296,079	T→C	T340A (ACT→GCT)	intF ←	CP4‑6 prophage; putative phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	296,079	0	T	C	100.0%	53.3 / NA	16	T340A (ACT→GCT)	intF	CP4‑6 prophage; putative phage integrase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/9);  total (7/9)

AACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGC  >  NC_000913/295962‑296214                                                                                                                      |                                                                                                                                        aaCGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCt                                                                                                                   <  2:180160/140‑1 (MQ=255)                                   aCTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCAtt                                                                                 >  1:341414/1‑140 (MQ=255)                                          aaaaCCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATc                                                                          <  1:347579/140‑1 (MQ=255)                                                                cGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGAc                                                    >  1:18145/1‑140 (MQ=255)                                                                              gATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACg                                      <  1:146552/140‑1 (MQ=255)                                                                                             tttAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTg                         <  1:59058/138‑1 (MQ=255)                                                                                             tttAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTg                         >  2:59058/1‑138 (MQ=255)                                                                                              ttAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAg                       <  1:47781/139‑1 (MQ=255)                                                                                              ttAACAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAg                       >  2:47781/1‑139 (MQ=255)                                                                                                aaCAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCaa                    <  1:164453/140‑1 (MQ=255)                                                                                                 aCAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCaaa                   <  2:206156/140‑1 (MQ=255)                                                                                                 aCAATTCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCaaa                   <  2:341414/140‑1 (MQ=255)                                                                                                     ttCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTa               >  2:137934/1‑140 (MQ=255)                                                                                                      tCAGAAACATAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTAc              >  1:35427/1‑140 (MQ=255)                                                                                                               tAAGGAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACACAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATa     >  2:278426/1‑140 (MQ=255)                                                                                                                  ggAGCGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGc  <  1:137934/140‑1 (MQ=255)                                                                                                                      |                                                                                                                                        AACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGC  >  NC_000913/295962‑296214

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑