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
A23 F171 I0 R2	49	45.2	1012374	92.5%	936445	139.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,361,590	C→T	55.0%	R239H (CGT→CAT)	secY1 ←	Sec family Type I general secretory pathway preprotein translocase SecY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,361,590	0	C	T	55.0%	1.5 / 46.6	38	R239H (CGT→CAT)	secY1	Sec family Type I general secretory pathway preprotein translocase SecY
Reads supporting (aligned to +/- strand): ref base C (9/8); new base T (8/13); total (17/21)
Fisher's exact test for biased strand distribution p-value = 5.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.47e-01

GTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGC  >  CP000730/2361452‑2361730

gTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGa                                                                                                                                            >  1:244434/1‑141 (MQ=255)

     aGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGc                                                                                                                                       <  1:45079/141‑1 (MQ=255)

      ggCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCt                                                                                                                                      >  1:385688/1‑141 (MQ=255)

            aagaagAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGt                                                                                                                                <  1:55331/141‑1 (MQ=255)

              gaagaaCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTAc                                                                                                                              >  1:59451/1‑141 (MQ=255)

                agaaCGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTATTAGAGGTAGATAAGTAGCCTGTGAACCTAATCCTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGTCTTCAAGTACAt                                                                                                                            >  2:94146/1‑141 (MQ=255)

                      ccATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAg                                                                                                                      >  2:340996/1‑141 (MQ=255)

                           gCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCt                                                                                                                 >  2:22400/1‑141 (MQ=255)

                            cAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTa                                                                                                                <  2:388947/141‑1 (MQ=255)

                            cAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTa                                                                                                                <  2:59451/141‑1 (MQ=255)

                              aaGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTCGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACa                                                                                                              <  2:432945/141‑1 (MQ=255)

                                gATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGt                                                                                                            >  2:384555/1‑141 (MQ=255)

                                    aCAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAAt                                                                                                        <  2:264317/141‑1 (MQ=255)

                                    aCAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAAt                                                                                                        <  1:307475/141‑1 (MQ=255)

                                     cAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATa                                                                                                       >  1:465707/1‑141 (MQ=255)

                                              cacCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAgag                                                                                              <  2:12042/141‑3 (MQ=255)

                                                       aGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTaaaa                                                                                     <  1:180922/141‑1 (MQ=255)

                                                         ttCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGt                                                                                   <  2:224197/141‑1 (MQ=255)

                                                           cACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTcc                                                                                 >  2:186100/1‑141 (MQ=255)

                                                                  aaaGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACt                                                                          >  1:319231/1‑141 (MQ=255)

                                                                   aaGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACtt                                                                         <  1:287544/141‑1 (MQ=255)

                                                                    aGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACttt                                                                        >  2:377950/1‑141 (MQ=255)

                                                                        aGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAAc                                                                    >  2:39014/1‑141 (MQ=255)

                                                                                   cTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAatga                                                         <  1:76792/141‑1 (MQ=255)

                                                                                                cTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGc                                            <  1:304777/141‑1 (MQ=255)

                                                                                                   tGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTCCAGAAACAGCACCTGCAGTTAATAGTATCAGTGACACCAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCa                                         <  1:478399/141‑1 (MQ=255)

                                                                                                   tGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCa                                                                  >  1:239031/1‑116 (MQ=255)

                                                                                                   tGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCa                                                                  <  2:239031/116‑1 (MQ=255)

                                                                                                     aGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCaac                                       >  1:396491/1‑141 (MQ=255)

                                                                                                         gtttgtttCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCaacgaac                                   <  1:492462/141‑1 (MQ=255)

                                                                                                            tgtttCTTAGCATATTGAATCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCa                                <  1:184930/141‑1 (MQ=255)

                                                                                                                   tAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTc                         <  2:307383/141‑1 (MQ=255)

                                                                                                                      cATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAATCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCaa                      <  1:340996/141‑1 (MQ=255)

                                                                                                                              aTCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAAtt              >  1:243511/1‑141 (MQ=255)

                                                                                                                               tCGGAATTTTATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTa             >  1:178093/1‑141 (MQ=255)

                                                                                                                                 ggAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTGTCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGa           <  2:181135/141‑1 (MQ=255)

                                                                                                                                      tttATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGActggc      >  2:203542/1‑141 (MQ=255)

                                                                                                                                      tttATGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGActggc      <  1:217171/141‑1 (MQ=255)

                                                                                                                                          cGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACtggctggc  <  2:244434/141‑1 (MQ=255)

                                                                                                                                          cGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACtggctggc  <  1:22400/141‑1 (MQ=255)

GTTCTAGGCAGTAAGAAGAACGCCATTGCAAAGATTACAGGAATAACACCGGCTGAGTTCACTTTTAAAGGTAGATAAGTTGCCTGTGAACCTAATCTTTGAGCAGTTTGTTTCTTAGCATATTGAATCGGAATTTTACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGC  >  CP000730/2361452‑2361730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A