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
A4 F28 I1 R1	162	93.0	3098984	99.0%	3067994	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,287,400	T→C	intergenic (+375/‑26)	agaI → / → yraH	putative deaminase AgaI/putative fimbrial protein YraH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,287,400	0	T	C	100.0%	128.7 / NA	35	intergenic (+375/‑26)	agaI/yraH	putative deaminase AgaI/putative fimbrial protein YraH
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (31/4); total (31/4)

TAATGAAAATATCAAATATTTGCATATAAATATAATCTTAAAGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGTACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGATTTTAAAATCC  >  NC_000913/3287270‑3287533

taATGAAAATATCAAATATTTGCATATAAATATAATCTTAAAGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTAc                                                                                                                              <  2:999826/140‑1 (MQ=255)

        atatCAAATATTTGCATATAAATATAATCTTAAAGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATaa                                                                                                                      >  1:939915/1‑140 (MQ=255)

                                 aaTCTTAAAGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACaaa                                                                                             >  2:1261526/1‑140 (MQ=255)

                                     ttAAAGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACa                                                                                         >  2:219848/1‑140 (MQ=255)

                                        aaGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCt                                                                                      >  1:777034/1‑140 (MQ=255)

                                             cAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGc                                                                                 >  1:691323/1‑140 (MQ=255)

                                             cAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGc                                                                                 >  2:166071/1‑140 (MQ=255)

                                                    tttAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTa                                                                          >  1:373227/1‑140 (MQ=255)

                                                           ttCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTgcgc                                                                   <  1:166071/140‑1 (MQ=255)

                                                            tCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCt                                                                  >  2:711579/1‑140 (MQ=255)

                                                            tCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCt                                                                  >  2:247384/1‑140 (MQ=255)

                                                                     tatTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAgg                                                         >  2:1203505/1‑140 (MQ=255)

                                                                             ccTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCg                                                 >  2:543852/1‑140 (MQ=255)

                                                                               tGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCt                                               <  1:219848/140‑1 (MQ=255)

                                                                                           aaaGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGt                                   >  2:607090/1‑140 (MQ=255)

                                                                                           aaaGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGt                                   >  2:1419702/1‑140 (MQ=255)

                                                                                           aaaGATGTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGt                                   >  1:1440497/1‑140 (MQ=255)

                                                                                                 gTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATa                             >  2:800220/1‑140 (MQ=255)

                                                                                                 gTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATa                             >  2:829364/1‑140 (MQ=255)

                                                                                                 gTTGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGACTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATa                             >  2:677962/1‑140 (MQ=255)

                                                                                                  ttGAACATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAg                            >  2:986015/1‑140 (MQ=255)

                                                                                                       cATATATTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGttttt                       >  1:919788/1‑140 (MQ=255)

                                                                                                          atatTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGAt                    >  2:100252/1‑140 (MQ=255)

                                                                                                          atatTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGAt                    >  2:358227/1‑140 (MQ=255)

                                                                                                          atatTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGAt                    >  2:755985/1‑140 (MQ=255)

                                                                                                          atatTCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGAt                    >  1:1054328/1‑140 (MQ=255)

                                                                                                              tCACATTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCg                <  1:1261526/140‑1 (MQ=255)

                                                                                                                 caTTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCgaga             >  2:594076/1‑140 (MQ=255)

                                                                                                                 caTTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCgaga             >  2:278908/1‑140 (MQ=255)

                                                                                                                  aTTAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGAt            >  1:292896/1‑140 (MQ=255)

                                                                                                                    tAAATATGATTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGAttt          >  1:543861/1‑140 (MQ=255)

                                                                                                                            aTTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGATTTTAAAATcc  >  2:658941/1‑140 (MQ=255)

                                                                                                                            aTTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGATTTTAAAATcc  >  2:213014/1‑140 (MQ=255)

                                                                                                                            aTTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGATTTTAAAATcc  >  2:1458627/1‑140 (MQ=255)

                                                                                                                            aTTATGCACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGATTTTAAAATcc  >  1:1427300/1‑140 (MQ=255)

TAATGAAAATATCAAATATTTGCATATAAATATAATCTTAAAGTTCAGTCTATTTAATGTTCAATGAAATATTTCTGCCTGTATAATCTTTAAAGATGTTGAACATATATTCACATTAAATATGATTATGTACTTGTTACAAGGATAAGGTTATATATGAATAAAGTTACAAAAACAGCTATTGCGGGCTTACTTGCGCTTTTCGCAGGTAATGCCGCTGCAACCGATGGTGAAATAGTTTTTGATGGCGAGATTTTAAAATCC  >  NC_000913/3287270‑3287533

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