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	2,517,962	A→G	33.9%	S371S (AGT→AGC)	spoT ←	bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,517,962	0	A	G	33.9%	32.4 / 25.7	50	S371S (AGT→AGC)	spoT	bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
Reads supporting (aligned to +/- strand): ref base A (21/12); new base G (4/13); total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.57e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.64e-01

GTGTGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGATTTGTGCGG  >  minE/2517898‑2518026

gtgtGAAAACGTAAATCTCATCCGGGTAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:2479134/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:1876568/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:2872218/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:3157037/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:3228674/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:2380122/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:98691/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:1562976/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:750849/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:1314561/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:738342/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAGCTAc                                                              <  1:1198218/69‑1 (MQ=255)

gtgtGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGATCTCGATAAATTCAAACGAGCTAc                                                              <  1:2927349/69‑1 (MQ=255)

  gtgAAAACGTAAATCTCATCCGGGAAGAGATCTGATTTAACGCTCTCGATAAATTCAAACGAACTACCg                                                            >  1:3200775/1‑69 (MQ=255)

     aaaaCGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGgcg                                                         >  1:3335838/1‑69 (MQ=255)

     aaaaCGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGgcg                                                         >  1:532846/1‑69 (MQ=255)

     aaaaCGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGgcg                                                         >  1:350685/1‑69 (MQ=255)

     aaaaCGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGgcg                                                         >  1:1740959/1‑69 (MQ=255)

     aaaaCGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGgcg                                                         >  1:493615/1‑69 (MQ=255)

       aaCGTAGATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGct                                                       >  1:3354066/1‑69 (MQ=255)

       aaCGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGct                                                       >  1:766604/1‑69 (MQ=255)

                      cGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTcc                                          >  1:1846833/1‑67 (MQ=255)

                      cGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTcc                                          >  1:1705868/1‑67 (MQ=255)

                         gAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTa                                                               >  1:1060187/1‑43 (MQ=255)

                         gAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCcagcag                                     >  1:954963/1‑69 (MQ=255)

                         gAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCcagcag                                     >  1:2962738/1‑69 (MQ=255)

                         gAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCcagcag                                     >  1:285223/1‑69 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:476491/69‑1 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:2647908/69‑1 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:1026750/69‑1 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:2529537/69‑1 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:2340461/69‑1 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:2797199/69‑1 (MQ=255)

                           agagATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGc                                   <  1:1285393/69‑1 (MQ=255)

                               aTCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTg                               >  1:3050321/1‑69 (MQ=255)

                                              ctcGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGgc                >  1:3024700/1‑69 (MQ=255)

                                              ctcGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGgc                >  1:1097637/1‑69 (MQ=255)

                                              ctcGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGgc                >  1:2494321/1‑69 (MQ=255)

                                              ctcGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGgc                >  1:1396489/1‑69 (MQ=255)

                                                   tAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGa           >  1:773934/1‑69 (MQ=255)

                                                   tAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGa           >  1:2649435/1‑69 (MQ=255)

                                                    aaaTTCAAACGAGCTACCGGCACTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGcgcgta           >  1:656632/1‑66 (MQ=255)

                                                    aaaTTCAAACGAGCTACCGGCACTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGTAt          >  1:1506476/1‑69 (MQ=255)

                                                    aaaTTCAAACGAGCTACCGGCACTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGTAt          >  1:2186710/1‑69 (MQ=255)

                                                    aaaTTCAAACGAGCTACCGGCACTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGTAt          >  1:650403/1‑69 (MQ=255)

                                                    aaaTTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGc                              <  1:103992/49‑1 (MQ=255)

                                                            aCGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGATTTGTGCgg  <  1:2784405/69‑1 (MQ=255)

                                                            aCGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGATTTGTGCgg  <  1:2189017/69‑1 (MQ=255)

                                                            aCGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGATTTGTGCgg  <  1:1958436/69‑1 (MQ=255)

                                                            aCGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGATTTGTGCgg  <  1:1723108/69‑1 (MQ=255)

GTGTGAAAACGTAAATCTCATCCGGGAAGAGATCGGATTTAACGCTCTCGATAAATTCAAACGAACTACCGGCGCTCTGTTGCAGCTCCAGCAGGCTTTGCATCCAGCGCTGGGCGCGGATTTGTGCGG  >  minE/2517898‑2518026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A