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 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,682,563	C→G	64.8%	R804P (CGG→CCG)	yfhM ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,682,563	0	C	G	64.8%	46.7 / 41.8	54	R804P (CGG→CCG)	yfhM	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (6/13); new base G (22/13); total (28/26)
Fisher's exact test for biased strand distribution p-value = 4.54e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.06e-01

TAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCC  >  minE/1682499‑1682631

tAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAAc                                                                  >  1:272625/1‑69 (MQ=255)

tAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAAc                                                                  >  1:2762746/1‑69 (MQ=255)

        gATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAAtct                                                          <  1:3435423/69‑1 (MQ=255)

                 gATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGccac                                                  <  1:938719/68‑1 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAAc                                                                  >  1:15008/1‑45 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:3323805/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:218052/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:2285791/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:2905618/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:300383/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:3007162/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:3066587/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:1093732/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:3371906/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:453420/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:630602/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:823180/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:988589/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:2072876/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:126938/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:1515174/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:1524248/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:157892/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:1729492/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:1909150/1‑46 (MQ=255)

                        ggTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCGGAACa                                                                 >  1:1992208/1‑46 (MQ=255)

                         gTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGc                                         <  1:2184202/69‑1 (MQ=255)

                                           gTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCg                          <  1:2780179/66‑1 (MQ=255)

                                           gTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCg                          <  1:2716400/66‑1 (MQ=255)

                                            tCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCg                          <  1:848840/65‑1 (MQ=255)

                                             cataTCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:1089757/65‑1 (MQ=255)

                                             cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:836061/68‑1 (MQ=255)

                                             cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:1741027/68‑1 (MQ=255)

                                             cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:2501134/68‑1 (MQ=255)

                                             cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:2259052/68‑1 (MQ=255)

                                             cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:632009/68‑1 (MQ=255)

                                             cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCa                      <  1:2002740/68‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGTGGCCCTTCACTGGa                              <  1:939785/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:3279624/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:2113030/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:1207457/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:2244202/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:1376181/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:2273171/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:2385388/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:3268368/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:3221619/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:3101401/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGa                              <  1:3100078/59‑1 (MQ=255)

                                              aGATCCAGCCCTTGAGCCGGAACATCAATCTCTTGCCACCACAGCGGCCCTTAACTGGa                              <  1:28523/59‑1 (MQ=255)

                                                  ccAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCAt                >  1:256807/1‑69 (MQ=255)

                                                  ccAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCAt                >  1:1715708/1‑69 (MQ=255)

                                                  ccAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCAt                >  1:1798858/1‑69 (MQ=255)

                                                  ccAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCAt                >  1:2536299/1‑69 (MQ=255)

                                                                cGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACccgcc  >  1:16286/1‑69 (MQ=255)

                                                                cGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACccgcc  >  1:2815115/1‑69 (MQ=255)

                                                                cGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACccgc   >  1:2811156/1‑68 (MQ=255)

TAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCC  >  minE/1682499‑1682631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A