Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A12 F28 I1 R1	176	31.5	1082462	98.8%	1069472	138.9

Breseq alignment

BRESEQ :: Evidence

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: `‑`

GATK/CNVnator alignment

N/A