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
A10 F1 I1 R1	759	65.2	3386260	90.7%	3071337	101.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	937,983	G→A	204 (TAG→TAA)	lolA →	lipoprotein chaperone

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	937,983	0	G	A	100.0%	92.2 / NA	29	204 (TAG→TAA)	lolA	lipoprotein chaperone
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (15/14); total (15/14)

AGTTTAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAGAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAG  >  NC_000913/937850‑938086

aGTTTAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCa                                                                                                    <  1:1370866/139‑1 (MQ=255)

    tAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCtg                                                                                                <  1:1481628/139‑1 (MQ=255)

            tGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCa                                                                                        >  2:113080/1‑139 (MQ=255)

                 cAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTg                                                                                   <  1:1650306/139‑1 (MQ=255)

                                 gcagTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCgg                                                                   >  2:1237273/1‑139 (MQ=255)

                                     ttATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGataa                                                               <  2:1289244/139‑1 (MQ=255)

                                       aTCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCtgagt                                                                                             <  2:703085/107‑1 (MQ=255)

                                       aTCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCtgagt                                                                                             >  1:703085/1‑107 (MQ=255)

                                                 aTCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAAcc                                                   >  1:1012685/1‑139 (MQ=255)

                                                 aTCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTGCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAAcc                                                   <  2:1012685/139‑1 (MQ=255)

                                                     attttgctgggggCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTg                                               >  2:73622/10‑139 (MQ=255)

                                                      aGCAAAATGGGGCTGTGGATGCAGCGAAATTTACTTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTACGTAAAGGcccc                                                                                                  <  2:979987/87‑1 (MQ=255)

                                                      aGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCAcc                                                                                                  >  1:979987/1‑87 (MQ=255)

                                                                  cTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGa                                                                  >  2:1426512/1‑107 (MQ=255)

                                                                  cTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGa                                                                  <  1:1426512/107‑1 (MQ=255)

                                                                                       ccTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTaaag                                                                                                       >  2:1265953/1‑49 (MQ=255)

                                                                                           cACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCtgagtga                                                                                           >  2:155162/1‑57 (MQ=255)

                                                                                           cACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCtgagtga                                                                                           <  1:155162/57‑1 (MQ=255)

                                                                                                cgccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACct                                                  <  2:315537/93‑1 (MQ=255)

                                                                                                cgccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACct                                                  >  1:315537/1‑93 (MQ=255)

                                                                                                  ccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                             >  2:627420/1‑96 (MQ=255)

                                                                                                  ccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                             <  2:986264/96‑1 (MQ=255)

                                                                                                  ccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                             >  1:986264/1‑96 (MQ=255)

                                                                                                  ccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                             <  1:627420/96‑1 (MQ=255)

                                                                                                  ccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAg  >  1:1372268/1‑139 (MQ=255)

                                                                                                  ccgcAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAg  >  1:1269862/1‑139 (MQ=255)

                                                                                                             cACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGAtttt                                                                       >  2:1439030/1‑59 (MQ=255)

                                                                                                             cACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGAtttt                                                                       <  1:1439030/59‑1 (MQ=255)

                                                                                                                            aCGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                             <  1:732720/70‑1 (MQ=255)

                                                                                                                            aCGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                             >  2:732720/1‑70 (MQ=255)

                                                                                                                              gtaagtaaAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACtttt                                                        <  2:1361809/57‑1 (MQ=255)

                                                                                                                              gtaagtaaAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACtttt                                                        >  1:1361809/1‑57 (MQ=255)

AGTTTAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAGAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAG  >  NC_000913/937850‑938086

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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