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 F8 I0 R2	296	77.6	4260404	88.1%	3753415	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,142,959	A→G	57.1%	N468D (AAC→GAC)	katE →	hydroperoxidase HPII(III)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,142,959	0	A	G	57.1%	27.7 / 69.9	56	N468D (AAC→GAC)	katE	hydroperoxidase HPII(III)
Reads supporting (aligned to +/- strand): ref base A (15/9); new base G (15/17); total (30/26)
Fisher's exact test for biased strand distribution p-value = 2.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.81e-01

CATCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATACCAGGAGCGCGTGGAA  >  minE/1142902‑1143027

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAAc                                                                    >  1:2976865/1‑60 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAAc                                                                    >  1:3986136/1‑60 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAAc                                                                    >  1:2601696/1‑60 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAAc                                                                    >  1:2538630/1‑60 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGa                                                         <  1:959948/71‑1 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGa                                                         <  1:645508/71‑1 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGa                                                         <  1:13538/71‑1 (MQ=255)

catCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGa                                                         <  1:3360789/71‑1 (MQ=255)

       tGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACAccg                                                  >  1:2567571/1‑71 (MQ=255)

       tGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACAcc                                                   >  1:1047140/1‑70 (MQ=255)

                 cacTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGAGGCCGa                                        <  1:545802/71‑1 (MQ=255)

                  acTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAacac                                                    >  1:451675/1‑58 (MQ=255)

                  acTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAacac                                                    >  1:1464009/1‑58 (MQ=255)

                  acTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGaaa                                                       >  1:1809419/1‑55 (MQ=255)

                  acTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGaaa                                                       >  1:1841420/1‑55 (MQ=255)

                  acTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGaaa                                                       >  1:3126520/1‑55 (MQ=255)

                  acTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGaaa                                                       >  1:3389379/1‑55 (MQ=255)

                   cTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGa                                        <  1:3065922/69‑1 (MQ=255)

                   cTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGa                                        <  1:4238937/69‑1 (MQ=255)

                   cTAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGa                                        <  1:1404550/69‑1 (MQ=255)

                    tAACCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAAc                                     >  1:832044/1‑71 (MQ=255)

                     aaCCCGGCGAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGaaa                                      >  1:2883381/1‑69 (MQ=255)

                          ggCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACgcggcg                               >  1:3261768/1‑71 (MQ=255)

                             gAATTACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGtt                            >  1:3351528/1‑71 (MQ=255)

                               aTTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGtttt                          <  1:4148347/71‑1 (MQ=255)

                               aTTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGtttt                          <  1:1819392/71‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAac                                                      <  1:3189392/42‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAac                                                      <  1:1011278/42‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAac                                                      <  1:988799/42‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAac                                                      <  1:2979928/42‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAac                                                      <  1:210044/42‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAac                                                      <  1:1935728/42‑1 (MQ=255)

                                ttACGAACCGAACTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTg                         <  1:596523/71‑1 (MQ=255)

                                 tACGAACCGAACTCGATTAACGATAACTGGCCGCGCGaaa                                                       >  1:2184110/1‑40 (MQ=255)

                                 tACGAACCGAACTCGATTAACGATAACTGGCCGCGCGaaa                                                       >  1:1573141/1‑40 (MQ=255)

                                   cgaaccgaacTCGATTAACGATGACTGGCCGCGCGaaa                                                       >  1:1179470/1‑38 (MQ=255)

                                   cgaaccgaacTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAAt                      <  1:1844072/71‑1 (MQ=255)

                                        cgaacTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTg                         <  1:3644605/63‑1 (MQ=255)

                                        cgaacTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATa                  <  1:3958656/70‑1 (MQ=255)

                                        cgaacTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:1237093/1‑71 (MQ=255)

                                        cgaacTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:2355720/1‑71 (MQ=255)

                                        cgaacTCGATTAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:4035914/1‑71 (MQ=255)

                                        cgaacTCGATAAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATa                  <  1:3953547/70‑1 (MQ=255)

                                         gaacTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAcc                <  1:1691895/71‑1 (MQ=255)

                                         gaacTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:4019383/1‑70 (MQ=255)

                                         gaacTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:3966013/1‑70 (MQ=255)

                                         gaacTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:2294305/1‑70 (MQ=255)

                                          aacTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATAc                 >  1:4087349/1‑69 (MQ=255)

                                                 ttAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGaaa                                      >  1:3093958/1‑41 (MQ=255)

                                                 ttAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGaaa                                      >  1:495706/1‑41 (MQ=255)

                                                 ttAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGaaa                                      >  1:196239/1‑41 (MQ=255)

                                                 ttAACGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATACCAGGAgcg         <  1:2194170/70‑1 (MQ=255)

                                                 ttAACGATGACTGCCCGCGCGAAACACCGCCTGGGCCGaaa                                      >  1:2825563/1‑41 (MQ=37)

                                                     cGATGACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATACCAGGAGCGCGTgg    <  1:1175587/71‑1 (MQ=255)

                                                      gATGACTGGCCGCGCGAAACACCTCCGGGGCCGAAACGCGGCGGTTTTGAATCATACCAGGAGCGCGTgg    <  1:1335123/70‑1 (MQ=255)

                                                       aTAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATACCAGGAGCGCGTGGaa  <  1:3096809/71‑1 (MQ=255)

CATCGCATGGGGATCGACACTAACCCGGCGAATTACGAACCGAACTCGATTAACGATAACTGGCCGCGCGAAACACCGCCGGGGCCGAAACGCGGCGGTTTTGAATCATACCAGGAGCGCGTGGAA  >  minE/1142902‑1143027

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A