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	2,349,443	C→A	45.7%	R735R (CGG→CGT)	polA ←	fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,349,443	0	C	A	45.7%	21.0 / 70.0	70	R735R (CGG→CGT)	polA	fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease
Reads supporting (aligned to +/- strand): ref base C (24/14); new base A (14/18); total (38/32)
Fisher's exact test for biased strand distribution p-value = 1.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.48e-01

ACGGCGTTGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAT  >  minE/2349383‑2349508

aCGGCGTTGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGat                                                           <  1:948419/69‑1 (MQ=255)

aCGGCGTTGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGat                                                           <  1:436052/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:995347/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:2910007/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:3105168/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:2056104/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:3347309/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:42473/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:433680/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:1811799/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:1776876/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:445402/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:531195/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:982133/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:580691/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:975850/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:1240321/69‑1 (MQ=255)

      ttGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:1482862/69‑1 (MQ=255)

        gCTCGCTGGTGAGGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTttc                                                   >  1:1862457/1‑69 (MQ=255)

        gCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTttc                                                   >  1:2755007/1‑69 (MQ=255)

        gCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTttc                                                   >  1:2560913/1‑69 (MQ=255)

        gCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTttc                                                   >  1:436840/1‑69 (MQ=255)

                  gACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGaa                                         <  1:1748792/69‑1 (MQ=255)

                  gACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGaa                                         <  1:2211873/69‑1 (MQ=255)

                  gACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGaa                                         <  1:226136/69‑1 (MQ=255)

                   aCGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAAt                                        >  1:1362508/1‑69 (MQ=255)

                   aCGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAAt                                        >  1:1740570/1‑69 (MQ=255)

                   aCGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAAt                                        >  1:1687976/1‑69 (MQ=255)

                   aCGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAAt                                        >  1:2148726/1‑69 (MQ=255)

                   aCGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAAt                                        >  1:3186143/1‑69 (MQ=255)

                   aCGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:1836148/56‑1 (MQ=255)

                        ttCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCg                                     >  1:2702786/1‑67 (MQ=255)

                        ttCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCg                                     >  1:2822775/1‑67 (MQ=255)

                        ttCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCg                                     >  1:2521640/1‑67 (MQ=255)

                        ttCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCg                                     >  1:3274208/1‑67 (MQ=255)

                        ttCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCg                                     >  1:703273/1‑67 (MQ=255)

                           cAGTGGCAAACCAAACACTTCTGCCGCCGTTGCACGGTGGATATCttt                                                     <  1:696293/48‑1 (MQ=255)

                                          cacTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAc                  >  1:2603208/1‑68 (MQ=255)

                                          cacTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAc                  >  1:957891/1‑68 (MQ=255)

                                          cacTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAc                  >  1:2741262/1‑68 (MQ=255)

                                          cacTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAc                  >  1:1506909/1‑68 (MQ=255)

                                          cacTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAACCCTTTGTCa                   >  1:1116076/1‑67 (MQ=255)

                                               ccgccgccGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGa              >  1:2477695/3‑67 (MQ=255)

                                               cTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGa              >  1:2627221/1‑67 (MQ=255)

                                               cTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGa              >  1:1145680/1‑67 (MQ=255)

                                               cTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGa              >  1:1159720/1‑67 (MQ=255)

                                               cTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGa              >  1:2058578/1‑67 (MQ=255)

                                                    gccgTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGa          <  1:2821662/66‑1 (MQ=255)

                                                    gccgTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGa          <  1:1117418/66‑1 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:552600/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:1177124/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:881915/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:1312398/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:622544/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:59803/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:589746/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:3110942/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:1432328/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:3094171/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:1641238/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcgc                >  1:1961999/1‑57 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcga                >  1:2395645/1‑56 (MQ=255)

                                                       gTTGCACGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCAcg                 >  1:1937065/1‑56 (MQ=255)

                                                         ttcccGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:365616/67‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:1590853/69‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:1380547/69‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:1300095/69‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:3318757/69‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:2949799/69‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:106486/69‑1 (MQ=255)

                                                         tGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAt  <  1:2264545/69‑1 (MQ=255)

                                                            ccGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGa          <  1:192442/58‑1 (MQ=255)

ACGGCGTTGCTCGCTGGTGACGGTTTCCAGTGGCAAACCAAACACTTCTGCCGCCGTTGCCCGGTGGATATCTTTTCCTTCCGCGAATGCGGTCAGCAAGCCTTTGTCACGCGAAAGATGCGCCAT  >  minE/2349383‑2349508

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