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 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,503,125	G→A	223 (TAG→TAA)	ydcL →	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,503,125	0	G	A	100.0%	64.7 / NA	21	223 (TAG→TAA)	ydcL	lipoprotein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (12/9); total (12/9)

GGTTATCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACG  >  NC_000913/1502990‑1503260

ggTTATCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTc                                                                                                                                      >  1:1350527/1‑139 (MQ=255)

                cgtCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGtt                                                                                                                      >  2:94315/1‑139 (MQ=255)

                                       gAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTgc                                                                                               >  2:241579/1‑139 (MQ=255)

                                             cGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTa                                                                                         <  1:94315/139‑1 (MQ=255)

                                                  gTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAAcc                                                                                    >  2:326749/1‑139 (MQ=255)

                                                           tGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                             >  2:531506/1‑89 (MQ=255)

                                                           tGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                             <  1:531506/89‑1 (MQ=255)

                                                                ttCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGAcgcg                                                                                                                              >  1:136035/1‑83 (MQ=255)

                                                                ttCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGAcgcg                                                                                                                              <  2:136035/83‑1 (MQ=255)

                                                                 tCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCg                                                                     <  1:1198636/139‑1 (MQ=255)

                                                                                            aCATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                             >  1:260737/1‑56 (MQ=255)

                                                                                            aCATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                             <  2:260737/56‑1 (MQ=255)

                                                                                                                   tttGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCa                                                                                 <  2:1044509/77‑1 (MQ=255)

                                                                                                                   tttGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCa                                                                                 >  1:1044509/1‑77 (MQ=255)

                                                                                                                   tttGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCaa                   <  1:241579/139‑1 (MQ=255)

                                                                                                                   tttGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCaa                   >  2:479811/1‑139 (MQ=255)

                                                                                                                            aaCAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAggg                                                                       >  2:108704/1‑78 (MQ=255)

                                                                                                                            aaCAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAggg                                                                       <  1:108704/78‑1 (MQ=255)

                                                                                                                            aaCAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAGTGTATTGGc          >  2:255727/1‑139 (MQ=255)

                                                                                                                             aCAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGttt                                                  >  2:162385/1‑98 (MQ=255)

                                                                                                                             aCAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGttt                                                  <  1:162385/98‑1 (MQ=255)

                                                                                                                                    gtaatTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACg  <  1:479811/139‑1 (MQ=255)

GGTTATCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACG  >  NC_000913/1502990‑1503260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A