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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,485,541	C→T	G93D (GGT→GAT)	yhfA ←	OsmC family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,485,541	0	C	T	97.1%	112.7 / NA	34	G93D (GGT→GAT)	yhfA	OsmC family protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (17/16); minor base G (0/1); total (17/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGTCACGCGGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGACCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGATCGAAACCACATCGATGGCAC  >  NC_000913/3485411‑3485676

aaGTCACGCGGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGt                                                                                                                                     <  1:120906/135‑1 (MQ=255)

aaGTCACGCGGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGt                                                                                                                                     >  2:120906/1‑135 (MQ=255)

aaGTCACGCGGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACg                                                                                                                                 >  1:617457/1‑139 (MQ=255)

   tCACGCGGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATa                                                                                                                              >  1:338806/1‑139 (MQ=255)

       gcgGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAAt                                                                                                                          >  1:304270/1‑139 (MQ=255)

        cgGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACg                                                                                                                                 >  1:116699/1‑131 (MQ=255)

        cgGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACg                                                                                                                                 <  2:116699/131‑1 (MQ=255)

        cgGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATg                                                                                                                         >  1:200701/1‑139 (MQ=255)

        cgGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACAATAAAATg                                                                                                                         >  2:585836/1‑139 (MQ=255)

                aCTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTaa                                                                                                                 <  1:183158/139‑1 (MQ=255)

                         gagtgagtAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTaa                                                                                                        >  2:614112/1‑139 (MQ=255)

                            tgagtAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACa                                                                                                     >  2:26140/1‑139 (MQ=255)

                            tgagtAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACa                                                                                                     >  1:366468/1‑139 (MQ=255)

                                tAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCg                                                                                                 <  2:617457/139‑1 (MQ=255)

                                     ttCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATa                                                                                                                              <  1:359941/105‑1 (MQ=255)

                                     ttCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATa                                                                                                                              >  2:359941/1‑105 (MQ=255)

                                               tttCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTcgcg                                                                                  <  1:77396/139‑1 (MQ=255)

                                                    aGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTcg                                                                                    >  1:355262/1‑132 (MQ=255)

                                                    aGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTcg                                                                                    <  2:355262/132‑1 (MQ=255)

                                                    aGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGtt                                                                             <  1:345939/139‑1 (MQ=255)

                                                           aCGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAAt                                                                                                                >  1:421678/1‑97 (MQ=255)

                                                           aCGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAAt                                                                                                                <  2:421678/97‑1 (MQ=255)

                                                                              ctcGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCg                                                   >  2:168404/1‑139 (MQ=255)

                                                                              ctcGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCg                                                   >  2:284476/1‑139 (MQ=255)

                                                                                cGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGAc                                                 <  2:338806/139‑1 (MQ=255)

                                                                                        agaTCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTaaa                                                                                                       >  1:500294/1‑77 (MQ=255)

                                                                                        agaTCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTaaa                                                                                                       <  2:500294/77‑1 (MQ=255)

                                                                                              aCCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGAGCGGTGACGATAATATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGTGGCGTTCAGAGGTCAATTTTACTTCACAAGCGACCACATCATTACGcc                                   <  1:617647/139‑1 (MQ=255)

                                                                                                  cACGCGCAACCGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCttt                               >  1:228154/1‑139 (MQ=255)

                                                                                                           ccGCTGCGTCTTTCAGGTCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGAt                      <  2:200701/139‑1 (MQ=255)

                                                                                                                    cTTTCAGGTCGCGATCGGTGACAATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGATCGAAACcac             <  1:585836/139‑1 (MQ=255)

                                                                                                                            tCGCGATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGATCGAAACCACATCGATgg     <  1:26140/139‑1 (MQ=255)

                                                                                                                              gcgATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGATCGAAACCACATCGATGGCa   <  2:228154/139‑1 (MQ=255)

                                                                                                                               cgATCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGATCGAAACCACATCGATGGCAc  <  2:304270/139‑1 (MQ=255)

AAGTCACGCGGCAACCACTTCATACGAGTGAGTAATATTCACCGCTTTTTCCAGCATCAACGCCACTGAACAATATTTCTCGGCAGAGAGATCAACCGCACGCGCAACCGCTGCGTCTTTCAGGTCGCGACCGGTGACGATAAAATGCAGATTAATGTGCGTAAACAGGCGTGGTGCCTCTTCGCGGCGTTCAGAGGTCAATTTTACTTCACAATCGACCACATCCTGACGCCCTTTTTGCAGGATCGAAACCACATCGATGGCAC  >  NC_000913/3485411‑3485676

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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