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 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

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%	63.3 / NA	21	223 (TAG→TAA)	ydcL	lipoprotein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (11/10); total (11/10)

ATCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATT  >  NC_000913/1502994‑1503249

aTCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGa                                                                                                                       >  1:485787/1‑139 (MQ=255)

  cAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGAcg                                                                                                                     <  1:417900/139‑1 (MQ=255)

     aGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                  <  2:485787/139‑1 (MQ=255)

          ttcgtCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCg                                                                                                             >  1:460075/1‑139 (MQ=255)

                                                              cGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTcc                                                                                                                          <  1:39321/74‑1 (MQ=255)

                                                              cGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTcc                                                                                                                          >  2:39321/1‑74 (MQ=255)

                                                                              gTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCACCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGt                                         >  2:845840/1‑139 (MQ=255)

                                                                               ttATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCTGTGCGCCGTAAAACCCCCTCCTTCAGGGCGGGGATATAAGGCGCGGtt                                        >  2:2808/1‑139 (MQ=255)

                                                                                   tgatgaCATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTcc                                    >  1:263623/1‑139 (MQ=255)

                                                                                     atgaCATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTg                                                                                     <  1:563281/88‑1 (MQ=255)

                                                                                     atgaCATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCAc                                  <  1:51863/139‑1 (MQ=255)

                                                                                     atgaCATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTGATCCGGTg                                                                                     >  2:563281/1‑88 (MQ=255)

                                                                                         cATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCg                                                          <  2:306167/111‑1 (MQ=255)

                                                                                         cATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCg                                                          >  1:306167/1‑111 (MQ=255)

                                                                                            ggCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTa                                                                              <  2:193061/88‑1 (MQ=255)

                                                                                            ggCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTa                                                                              >  1:193061/1‑88 (MQ=255)

                                                                                                            aTGTTTGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTgttgtt           <  2:263623/139‑1 (MQ=255)

                                                                                                             tGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                  <  1:654223/35‑1 (MQ=255)

                                                                                                             tGTTTGACGTTAACAAAAAGTAATTCCAGACgcgc                                                                                                                  >  2:654223/1‑35 (MQ=255)

                                                                                                                ttGACGTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAAt       <  2:460075/139‑1 (MQ=255)

                                                                                                                     gTTAACAAAAAGTAATTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTAtt  >  2:400836/1‑139 (MQ=255)

ATCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATT  >  NC_000913/1502994‑1503249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A