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
A9 F1 I1 R1	759	71.0	3673240	91.5%	3361014	104.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,426,023	A→G	pseudogene (394/453 nt)	ydaY →	pseudogene, Rac prophage,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,426,023	0	A	G	100.0%	161.6 / NA	46	pseudogene (394/453 nt)	ydaY	pseudogene, Rac prophage,Phage or Prophage Related
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/25); total (21/25)

ATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACGTTATGCTGGAA  >  NC_000913/1425889‑1426148

aTCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAg                                                                                                                           >  1:106859/1‑139 (MQ=255)

                       cTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACt                                                                                                    <  2:1715541/139‑1 (MQ=255)

                             gAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGtt                                                                                              <  1:1555908/139‑1 (MQ=255)

                                gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGcc                                                                                           >  2:944672/1‑139 (MQ=255)

                                gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGcc                                                                                           >  1:293302/1‑139 (MQ=255)

                                gcagcCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGcc                                                                                           >  1:488727/1‑139 (MQ=255)

                                      agcATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGtt                                                                                              >  2:786218/1‑130 (MQ=255)

                                      agcATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGtt                                                                                              <  1:786218/130‑1 (MQ=255)

                                              ccAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAAc                                                                             <  1:164006/139‑1 (MQ=255)

                                                           cagcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAccc                                                                >  2:1221504/1‑139 (MQ=255)

                                                            agcagAAGCAGGATACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCAcc                                                                                        >  1:987249/1‑114 (MQ=255)

                                                            agcagAAGCAGGAAACGATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCAcc                                                                                        <  2:987249/114‑1 (MQ=255)

                                                                            gATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAAc                                                                             >  2:1560250/1‑109 (MQ=255)

                                                                            gATAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAAc                                                                             <  1:1560250/109‑1 (MQ=255)

                                                                              tAAAAAAGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGttgttg                                             <  2:1629089/139‑1 (MQ=255)

                                                                                   aaGCCATAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGACACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGc                                        <  2:106859/139‑1 (MQ=255)

                                                                                      ccATAACTGCCCAGCGGGGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTa                                     <  1:660638/139‑1 (MQ=255)

                                                                                        aTAACTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt                                   <  2:1801060/139‑1 (MQ=255)

                                                                                               cccAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGACAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 <  1:1293831/86‑1 (MQ=255)

                                                                                               cccAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 >  1:379234/1‑86 (MQ=255)

                                                                                               cccAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 <  2:379234/86‑1 (MQ=255)

                                                                                               cccAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 >  2:1293831/1‑86 (MQ=255)

                                                                                                    cGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAcc                                                                 >  2:963674/1‑97 (MQ=255)

                                                                                                    cGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGAcc                                                                 <  1:963674/97‑1 (MQ=255)

                                                                                                      gtggtTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGt                     >  2:1431102/1‑139 (MQ=255)

                                                                                                         gtTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAgt                                                  >  2:318859/1‑107 (MQ=255)

                                                                                                         gtTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAgt                                                  <  1:318859/107‑1 (MQ=255)

                                                                                                         gtTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTa                                     >  1:720883/1‑120 (MQ=255)

                                                                                                         gtTATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTa                                     <  2:720883/120‑1 (MQ=255)

                                                                                                          ttATCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGccc                 <  1:116809/139‑1 (MQ=255)

                                                                                                            aTCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 >  1:811752/1‑73 (MQ=255)

                                                                                                            aTCGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 <  2:811752/73‑1 (MQ=255)

                                                                                                              cGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACg             <  1:1431102/139‑1 (MQ=255)

                                                                                                              cGGAGTTCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACg             <  2:488727/139‑1 (MQ=255)

                                                                                                                   ttCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 <  2:42238/66‑1 (MQ=255)

                                                                                                                   ttCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 >  1:42238/1‑66 (MQ=255)

                                                                                                                   ttCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCgg                                                              <  1:578404/85‑1 (MQ=255)

                                                                                                                   ttCGGGGGAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCgg                                                              >  2:578404/1‑85 (MQ=255)

                                                                                                                       ggggAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACGTTATGCTgg    >  2:355878/1‑139 (MQ=255)

                                                                                                                        gggAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt                                   >  1:755553/1‑107 (MQ=255)

                                                                                                                        gggAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTAtt                                   <  2:755553/107‑1 (MQ=255)

                                                                                                                         ggAGAAAGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACGTTATGCTGGaa  <  1:944672/139‑1 (MQ=255)

                                                                                                                             aaaGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACGTTATg        <  2:196354/129‑1 (MQ=255)

                                                                                                                             aaaGGGGGGGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACGTTATg        >  1:196354/1‑129 (MQ=255)

                                                                                                                                  ggggGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 <  1:1038228/51‑1 (MQ=255)

                                                                                                                                  ggggGAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCg                                                                                 >  2:1038228/1‑51 (MQ=255)

ATCCAGAGTTGTACTGGCAGATCCTTGCAGAAGCAGCCAGCATCGCCCAGGGTAAAGAGCAGCAGAAGCAGGATACGATAAAAAAGCCATAGCTGCCCAGCGGTGGTTATCGGAGTTCGGGGGAGAAAGGGGGGAAAAGGCAAGATGGAAGCGAGAAAAACTCAGGTTGCCACCGATACCGGAACCAGAAATAGACCCGGTGCTTAAGGAGTTGTTGTACGCCTATTCGGTAATATCCCGTGCCCGACGTTATGCTGGAA  >  NC_000913/1425889‑1426148

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A