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	1,478,970	G→A	42.2%	G319G (GGC→GGT)	glpT ←	sn‑glycerol‑3‑phosphate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,478,970	0	G	A	42.2%	16.3 / 35.3	52	G319G (GGC→GGT)	glpT	sn‑glycerol‑3‑phosphate transporter
Reads supporting (aligned to +/- strand): ref base G (19/11); new base A (7/15); total (26/26)
Fisher's exact test for biased strand distribution p-value = 4.83e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01

AACGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCA  >  minE/1478913‑1479033

aaCGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGAc                                                      >  1:945449/1‑69 (MQ=255)

aaCGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGAc                                                      >  1:735796/1‑69 (MQ=255)

aaCGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGAc                                                      >  1:2695186/1‑69 (MQ=255)

aaCGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGAc                                                      >  1:3083280/1‑69 (MQ=255)

aaCGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGAc                                                      >  1:1794214/1‑69 (MQ=255)

  ggATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACAACGAAAGACtt                                                    >  1:246290/2‑69 (MQ=255)

  cGATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACCACGaaa                                                         >  1:1734312/1‑64 (MQ=255)

  cGATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACCACGAAAGACtt                                                    >  1:563778/1‑69 (MQ=255)

  cGATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACCACGAAAGACtt                                                    >  1:1674711/1‑69 (MQ=255)

  cGATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACCACGAAAGACtt                                                    >  1:3197476/1‑69 (MQ=255)

  cGATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACCACGAAAGACtt                                                    >  1:3101852/1‑69 (MQ=255)

  cGATAGTCGCGATGGTCACCAGTGTCATAAAGAAGACGCCGGTTGCCCCACGGTTACCACGAAAGACtt                                                    >  1:692577/1‑69 (MQ=255)

     tAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTAt                                                 >  1:3224017/1‑69 (MQ=255)

     tAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTAt                                                 >  1:596511/1‑69 (MQ=255)

     tAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTAt                                                 >  1:2664932/1‑69 (MQ=255)

     tAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTAt                                                 >  1:2505229/1‑69 (MQ=255)

     tAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTAt                                                 >  1:1043853/1‑69 (MQ=255)

                            aTAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCaga                          >  1:1386960/1‑69 (MQ=255)

                            aTAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCaga                          >  1:2025565/1‑69 (MQ=255)

                            aTAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCaga                          >  1:259817/1‑69 (MQ=255)

                              aaaGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGt                        <  1:978088/69‑1 (MQ=255)

                               aaGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGt                        <  1:747628/68‑1 (MQ=255)

                               aaGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGt                        <  1:1313634/68‑1 (MQ=255)

                                      cGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGaa                <  1:2284370/69‑1 (MQ=255)

                                      cGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGaa                <  1:2620254/69‑1 (MQ=255)

                                      cGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGaa                <  1:757020/69‑1 (MQ=255)

                                      cGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGaa                <  1:1611571/69‑1 (MQ=255)

                                       gCCGGTTGCCCCACTGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAAt               <  1:1207139/69‑1 (MQ=255)

                                       gCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAAt               <  1:462235/69‑1 (MQ=255)

                                            ttGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTg          <  1:848708/69‑1 (MQ=255)

                                             tGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTg          <  1:2814948/68‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:1137752/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:240186/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:622767/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:1385592/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:155444/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:3353657/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:1952052/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:3139732/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:3125091/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:1957558/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:2939751/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:2760298/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:2225549/69‑1 (MQ=255)

                                                   aCGGTTACCACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:2539806/69‑1 (MQ=255)

                                                   aCGGTTACAACGAAAGACTTTATCCGACATCCAGCCGCACAGCAGGGTGCCCGGAATACCTGCATATTc   <  1:715232/69‑1 (MQ=255)

                                                      gTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCa  >  1:311686/1‑67 (MQ=255)

                                                      gTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCa  >  1:215131/1‑67 (MQ=255)

                                                      gTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCa  >  1:125471/1‑67 (MQ=255)

                                                      gTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCa  >  1:794664/1‑67 (MQ=255)

                                                      gTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCa  >  1:2253333/1‑67 (MQ=255)

                                                      gTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCa  >  1:966468/1‑67 (MQ=255)

AACGATAGTCGCGATGGTCACCAGTGTCATAAAGAAAACGCCGGTTGCCCCACGGTTGCCACGGAAGACTTTATCCGACATCCAGCCGCACAGCAGAGTGCCCGGAATACCTGCATATTCA  >  minE/1478913‑1479033

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