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
A13 F121 I0 R1	43	32.8	695000	96.9%	673455	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,775,439	C→T	62.6%	G362D (GGT→GAT)	clpX ←	S14 family endopeptidase ClpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,775,439	0	C	T	62.6%	22.0 / 16.0	26	G362D (GGT→GAT)	clpX	S14 family endopeptidase ClpX
Reads supporting (aligned to +/- strand): ref base C (3/7); new base T (10/6); total (13/13)
Fisher's exact test for biased strand distribution p-value = 2.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCGTCGTATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTT  >  CP000730/1775300‑1775559

tGCGTCGTATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCAcc                                                                                                                         >  1:238734/1‑141 (MQ=255)

   gtcgtATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGt                                                                                                                      <  1:5229/141‑1 (MQ=255)

    tcgtATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTTCCGCTTCTTCTATGATTTGACGTATACCACGGGGACCTGtt                                                                                                                     >  1:260102/1‑141 (MQ=255)

                    cAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCtt                                                                                                     >  1:315101/1‑141 (MQ=255)

                          ttttcttAATTGTTTGTCCTGTAATAACTACCTTCGTTACATTTTCGTTCGCAGGCACATCAAACATAATATCGATTAACGATTCTTTTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCAc                                                                                               <  2:110225/136‑1 (MQ=255)

                           ttcATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACt                                                                                              >  1:3379/1‑141 (MQ=255)

                                catttgtttgtGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTg                                                                                         <  2:346133/138‑1 (MQ=255)

                                        tgtgCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCGCTAATTGCTGATaaa                                                                                 >  2:110546/1‑141 (MQ=255)

                                          ggCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGc                                                                               <  1:181821/140‑1 (MQ=255)

                                                aataaCTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCttcttc                                                                         <  1:314130/141‑1 (MQ=255)

                                                      tACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTAATAAAGCTTCGTCAGTGaa                                                                   >  1:174779/1‑141 (MQ=255)

                                                          ttCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAActct                                                               >  1:240520/1‑141 (MQ=255)

                                                                   ttttCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGGTTGAACGTAAACCACGCGCATCTGTTTTTCATATTTTTTTGTTTTCACTAATTGCTGATAAAGGTTCTTCAGTGAACTCTTAATCtaca                                                      >  1:148957/1‑141 (MQ=255)

                                                                         ttAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACTACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGATTCTTCAGTGAACTCTAAATCCACATCATCt                                                >  1:207515/1‑141 (MQ=255)

                                                                            gAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAAt                                             >  1:277819/1‑141 (MQ=255)

                                                                               ggCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTcc                                          <  2:315101/141‑1 (MQ=255)

                                                                               ggCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTcc                                          <  2:238734/141‑1 (MQ=255)

                                                                                 cacaTCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAg                                        >  2:125763/1‑141 (MQ=255)

                                                                                         aCATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAg                                >  1:47701/1‑141 (MQ=255)

                                                                                           ataataTCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGta                              <  1:90637/141‑1 (MQ=255)

                                                                                                        aCGATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACaa                 <  1:203325/141‑1 (MQ=255)

                                                                                                          gATTCTTCTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGt               <  2:311578/141‑1 (MQ=255)

                                                                                                            ttcttcTATGATTGAACGTAAACCACGCGCATCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCAACATCATCTTATTCCAGCAGTTTAGTATATTGTTTCACAAGTGc             >  1:93735/1‑141 (MQ=255)

                                                                                                             tcttctATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTATTCAGTTAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCa            >  1:323334/1‑141 (MQ=255)

                                                                                                                 ctATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTCCGAGTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCAtttt        <  1:233371/141‑1 (MQ=255)

                                                                                                                  tATGATTGAACGTACACCACGCTCACCTTTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATTAAGCTTCTTCAGTTAGCTCTAAATCCTCATCATCTCATTCCAGCATTTTAGTATATTGTTTCACAAGTGCAttttt       <  2:300605/141‑1 (MQ=255)

                                                                                                                       tagaccctAAACCACGCGCACCTGTTTTTCTTTTAATTGCTTTTTCACTAATTGCTGATTAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGtt  <  2:329644/134‑1 (MQ=255)

TGCGTCGTATAGTTCTGGTTCAGTTTCTTCATTAATTGTTTGTGCTGTAATAACTACCTTCGTTACATTTTCGTTAGAAGGCACATCAAACATAATATCGATTAACGATTCTTCTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTT  >  CP000730/1775300‑1775559

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A