Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,071,643	T→C	G35G (GGT→GGC)	flu →	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,071,643	0	T	C	100.0%	95.8 / NA	27	G35G (GGT→GGC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (14/13);  total (14/13)

TTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACGACCA  >  NC_000913/2071506‑2071779                                                                                                                                          |                                                                                                                                         ttttttATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACgtggcggcgt                                                                                                                                        <  2:370449/140‑1 (MQ=255)          cACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGc                                                                                                                               >  2:53456/1‑140 (MQ=255)           aCCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCa                                                                                                                              <  2:123529/140‑1 (MQ=255)             ccTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACt                                                                                                                            >  1:202767/1‑140 (MQ=255)                     tAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTg                                                                                                                    <  1:53456/140‑1 (MQ=255)                      aaGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGc                                                                                                                   <  1:403261/140‑1 (MQ=255)                       aGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGGTGGGCTGTCTCTTTcc                                                                                                                  >  2:403261/1‑140 (MQ=255)                       aGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTAGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTTGACCGTTTCTTTcc                                                                                                                  >  1:264699/1‑140 (MQ=255)                            aaGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACCGTCTCTTGTCGccgg                                                                                                             >  2:480092/1‑137 (MQ=255)                             aGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCGccggc                                                                                                            >  2:146275/1‑136 (MQ=255)                             aGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCA‑GGGGTAAACGTGGCGGCGTGGCGGGTGCACTGTCTCTTTCCCCAgtca                                                                                                           >  2:146501/1‑140 (MQ=255)                                      aaCGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTc                                                                                                   <  2:202767/140‑1 (MQ=255)                                                           aCAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATc                                                                              >  1:505961/1‑140 (MQ=255)                                                             aGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTTCCGCCGTCACGTCCCTCCCCGGGCTGGCTGCTGGCATcct                                                                            >  2:345457/1‑138 (MQ=255)                                                               gCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGGTGGCCTGTCTCCTTGCGCAGGCCCGCCACTCCCCGGGCTGGCTGCCGACAACggtt                                                                          >  2:468108/1‑137 (MQ=255)                                                                 gagacaggAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTtgtg                                                                        <  1:44401/134‑1 (MQ=255)                                                                    tATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCAc                                                                     <  2:405618/140‑1 (MQ=255)                                                                                   cGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGGACTGTCTCTTGCCGCAGTCACGTCACTCCCGGGGGTGGCTGCTGGCATCGTTTTGCACCCGGgggactgtctc                                                      >  2:44401/1‑133 (MQ=255)                                                                                   cGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCCCTGTCTCTTTCCCCCGTCACGGCCCTCCCCGGGCCGGGCGCTGACATCGTTTTGGCCCCCGGGGGAACCggg                                                      >  2:127818/1‑138 (MQ=255)                                                                                    gggCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCA‑GGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGaa                                                    <  1:146501/140‑1 (MQ=255)                                                                                         cTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAAcggc                                                <  2:505961/140‑1 (MQ=255)                                                                                          tttCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAAcggcg                                               <  1:437644/140‑1 (MQ=255)                                                                                               tGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAaca                                          <  1:257934/140‑1 (MQ=255)                                                                                                   tGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTgg                                      <  1:468108/140‑1 (MQ=255)                                                                                                    gCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTTCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGGGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGc                                     >  1:278119/1‑140 (MQ=255)                                                                                                    gCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGc                                     <  2:128603/140‑1 (MQ=255)                                                                                                    gCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGGTGCACCGTCTCTTGCCGCCGCCACCTCACTCCCGGCGCTGGCCGCCGGCATCGTTGTTCCCCCCGGGGAAACCGGGGACAGCGGCACACTggg                                     >  2:149393/1‑139 (MQ=255)                                                                                                             cTGGCCCGCGCACGGGGTAAACGTGGCGGCGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGa                            <  1:127818/140‑1 (MQ=255)                                                                                                                                      gcggcgtggcggtTGCACTGTCTCTTTCCCCAGGCACCTCACTCCCCGGGCTGGGCGCTGGCATCGTTGTGCACCCGGGGGAAACCGTGAAAGGGGGAAAACTGGCAAATCATGACAAACAGATTGTCTTCGGTACGAcc   >  2:26741/1‑140 (MQ=255)                                                                                                                                      gcggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCCGGGCTGGCTGCTGACATCGTTTTGCACCCGGGGGAAAACGGGAACGGCGGGACACTGGCCAAACATGACAACCAGATTGTCTTCGGGACGAcc   >  2:228268/1‑140 (MQ=255)                                                                                                                                       cggcgtggcggtTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACGACCa  <  1:228268/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                         TTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAAACGTGGCGGTGTGGCGGTTGCACTGTCTCTTGCCGCAGTCACGTCACTCCCGGTGCTGGCTGCTGACATCGTTGTGCACCCGGGAGAAACCGTGAACGGCGGAACACTGGCAAATCATGACAACCAGATTGTCTTCGGTACGACCA  >  NC_000913/2071506‑2071779

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: ‑