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
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	412,492	C→T	75.9%	intergenic (‑137/+152)	leuS ← / ← lnt	leucyl‑tRNA synthetase/apolipoprotein N‑acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	412,492	0	C	T	75.9%	126.0 / 40.4	76	intergenic (‑137/+152)	leuS/lnt	leucyl‑tRNA synthetase/apolipoprotein N‑acyltransferase
Reads supporting (aligned to +/- strand): ref base C (6/12); new base T (26/31); total (33/43)
Fisher's exact test for biased strand distribution p-value = 4.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01

TAGCATAGCCCAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGTCTATTA  >  minE/412423‑412556

tagcatagcCCAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACt                                                                 >  1:2326982/1‑71 (MQ=255)

  gcatagcCCAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCa                                                               <  1:642432/71‑1 (MQ=255)

    atagcCCAAACGTCCGCGTCAAAACAGCCTTTCGAGCACTCGACGTTGAAATGATGCCCGGATTACTCATa                                                             <  1:4961584/71‑1 (MQ=255)

         ccAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACAtt                                                         >  1:2206665/1‑70 (MQ=255)

         ccAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACAt                                                          >  1:5336086/1‑69 (MQ=255)

          cAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTaa                                                       <  1:2715636/71‑1 (MQ=255)

             aCGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAAtt                                                     >  1:4577263/1‑70 (MQ=255)

                    cgTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTa                                                   >  1:844274/1‑65 (MQ=255)

                     gTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGtt                                            <  1:3676079/71‑1 (MQ=255)

                     gTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGtt                                            <  1:180503/71‑1 (MQ=255)

                      tCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGtt                                            <  1:4877106/70‑1 (MQ=255)

                       cAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCAt                                                              <  1:3405710/51‑1 (MQ=255)

                       cAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCAt                                                              <  1:5648191/51‑1 (MQ=255)

                       cAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          >  1:729654/1‑71 (MQ=255)

                        aaaaCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtgt                                         >  1:1503227/1‑71 (MQ=255)

                        aaaaCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtgt                                         >  1:1580744/1‑71 (MQ=255)

                        aaaaCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtgt                                         >  1:2987422/1‑71 (MQ=255)

                        aaaaCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtgt                                         >  1:1291069/1‑71 (MQ=255)

                        aaaaCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtgt                                         >  1:421930/1‑71 (MQ=255)

                           aCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCa                                                               >  1:5335531/1‑46 (MQ=255)

                           aCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTggg                                      <  1:4852558/71‑1 (MQ=255)

                           aCAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTggg                                      <  1:3734854/71‑1 (MQ=255)

                             aGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCg                                    <  1:2530201/71‑1 (MQ=255)

                             aGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCg                                    <  1:2131257/71‑1 (MQ=255)

                               ccTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTa                                  >  1:344460/1‑71 (MQ=255)

                                 tttCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:2806021/61‑1 (MQ=255)

                                  ttCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          >  1:4885043/1‑60 (MQ=255)

                                  ttCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          >  1:2843111/1‑60 (MQ=255)

                                  ttCGCGCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          >  1:4846850/1‑60 (MQ=255)

                                   tCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTtgtg                                        >  1:2144107/1‑61 (MQ=255)

                                   tCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTAtt                                <  1:3699574/69‑1 (MQ=255)

                                    cgcgCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTag                              >  1:2248100/1‑70 (MQ=255)

                                    cgcgCACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTag                              >  1:4062942/1‑70 (MQ=255)

                                     gcgcACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTagca                            <  1:5074996/71‑1 (MQ=255)

                                       gcACTCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTagcaaa                          <  1:1021645/71‑1 (MQ=255)

                                           tCGACGTTGAAATGATGCCCGGATTATTCATACATTaa                                                       <  1:1169618/38‑1 (MQ=255)

                                           tCGACGTTGAAATGATGCCCGGATTATTCATACATTaa                                                       <  1:2528874/38‑1 (MQ=255)

                                           tCGACGTTGAAATGATGCCCGGATTATTCATACATTaa                                                       <  1:1974760/38‑1 (MQ=255)

                                           tCGACGTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:4347337/51‑1 (MQ=255)

                                            cGACGTTGAAATGATGCCCGGATTAATCATACATTAATTTACAGAGttt                                           >  1:2381045/1‑49 (MQ=255)

                                             gACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAg                     >  1:1897383/1‑70 (MQ=255)

                                                gTTGAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAAc                 <  1:4589915/71‑1 (MQ=255)

                                                   gAAATGATGCCCGGATTATTCATACATTAATTTACaga                                               >  1:2130704/1‑38 (MQ=255)

                                                   gAAATGATGCCCGGATTATTCATACATTAATTTACaga                                               >  1:4063028/1‑38 (MQ=255)

                                                   gAAATGATGCCCGGATTATTCATACATTAATTTACaga                                               >  1:400808/1‑38 (MQ=255)

                                                   gAAATGATGCCCGGATTATTCATACATTAATTTACaga                                               >  1:2137497/1‑38 (MQ=255)

                                                   gAAATGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACa                >  1:2324802/1‑69 (MQ=255)

                                                   gAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACaa               <  1:3279365/70‑1 (MQ=255)

                                                    aaaTGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACa                >  1:4306920/1‑68 (MQ=255)

                                                    aaaTGATGCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAg             <  1:5344258/71‑1 (MQ=255)

                                                     aaTGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCg                                    <  1:3095692/47‑1 (MQ=255)

                                                     aaTGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCg                                    <  1:3639654/47‑1 (MQ=255)

                                                      atgatgCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:5513810/40‑1 (MQ=255)

                                                      atgatgCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:4759444/40‑1 (MQ=255)

                                                      atgatgCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:2216255/40‑1 (MQ=255)

                                                      atgatgCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:4946332/40‑1 (MQ=255)

                                                      atgatgCCCGGATTATTCATACATTAATTTACAGAGTTtg                                          <  1:3924765/40‑1 (MQ=255)

                                                       tgatgCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACa                <  1:3646591/65‑1 (MQ=255)

                                                         atgCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAg             <  1:674435/66‑1 (MQ=255)

                                                         atgCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAg             <  1:3945511/66‑1 (MQ=255)

                                                         atgCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAg             <  1:3912742/66‑1 (MQ=255)

                                                         atgCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAg             <  1:3242045/66‑1 (MQ=255)

                                                         atgCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGt        >  1:3403161/1‑71 (MQ=255)

                                                         atgCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGt        >  1:3396656/1‑71 (MQ=255)

                                                          tgCCCGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGTc       <  1:4616086/71‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGc                                     <  1:4478987/37‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGc                                     <  1:1155645/37‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGc                                     <  1:19588/37‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGc                                     <  1:398898/37‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGt                                   <  1:3819559/39‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGt                                   <  1:2277265/39‑1 (MQ=255)

                                                              cGGATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGTCta     >  1:4755249/1‑69 (MQ=255)

                                                               ggATTATTCATACATTAATTTACAGAGTTTGTGGGCGTa                                  >  1:2244866/1‑39 (MQ=255)

                                                               ggATTATTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGTCtatta  <  1:1120827/71‑1 (MQ=255)

                                                                gATTATTCATACATTAATTTACAGAGTTTGTGGGCGTAt                                 >  1:4611183/1‑39 (MQ=255)

                                                                 attattCATACATTAATTTACAGAGTTTGTGGGCGTATTagcaaagca                       >  1:3560382/1‑48 (MQ=255)

                                                                 attattCATACATTAATTTACAGAGTTTGTGGGCGTATTagcaaagca                       >  1:946447/1‑48 (MQ=255)

                                                                 attattCATACATTAATTTACAGAGTTTGTGGGCGTATTagcaaagc                        <  1:4651875/47‑1 (MQ=255)

                                                                 attattCATACATTAATTTACAGAGTTTGTGGGCGTATTagcaaagc                        <  1:213210/47‑1 (MQ=255)

                                                                    aCTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGaa           >  1:154066/1‑57 (MQ=255)

TAGCATAGCCCAAACGTCCGCGTCAAAACAGCCTTTCGCGCACTCGACGTTGAAATGATGCCCGGATTACTCATACATTAATTTACAGAGTTTGTGGGCGTATTAGCAAAGCAAGGAACAAAGAACGTCTATTA  >  minE/412423‑412556

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A