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	740,600	G→T	57.4%	T69T (ACC→ACA)	fhuE ←	ferric‑rhodotorulic acid outer membrane transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	740,600	0	G	T	57.4%	11.6 / 54.1	54	T69T (ACC→ACA)	fhuE	ferric‑rhodotorulic acid outer membrane transporter
Reads supporting (aligned to +/- strand): ref base G (17/6); new base T (13/18); total (30/24)
Fisher's exact test for biased strand distribution p-value = 2.75e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

CTTCCATCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGT  >  minE/740533‑740656

cTTCCATCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTgg                                                         >  1:3238381/1‑69 (MQ=255)

cTTCCATCCGATGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTgg                                                         >  1:3193766/1‑69 (MQ=255)

     aTCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTgg                                                         <  1:2627583/64‑1 (MQ=255)

     aTCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGt                                                        <  1:2858671/65‑1 (MQ=255)

     aTCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGt                                                        <  1:1583360/65‑1 (MQ=255)

     aTCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGt                                                        <  1:1772849/65‑1 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:1204978/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:73468/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:3258400/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:3219051/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:2843407/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:2628113/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:2619813/1‑68 (MQ=255)

                  tAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGAc                                        >  1:2605515/1‑68 (MQ=255)

                        tAGTGCCCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGt                                      >  1:2348783/1‑64 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:225144/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:2211136/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:860008/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:2951435/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:2944644/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:1658391/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:2793733/1‑68 (MQ=255)

                        tAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACgt                                 >  1:2710157/1‑68 (MQ=255)

                          gTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCt                                >  1:426427/1‑68 (MQ=255)

                          gTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCt                                >  1:1272452/1‑68 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCAtt                       >  1:842560/1‑59 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca             >  1:2327669/1‑69 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca             >  1:1129668/1‑69 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca             >  1:2336102/1‑69 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca             >  1:3383810/1‑69 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca             >  1:96843/1‑69 (MQ=255)

                                            tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca             >  1:1296811/1‑69 (MQ=255)

                                             cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat            >  1:2578302/1‑69 (MQ=255)

                                             cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat            >  1:1522627/1‑69 (MQ=255)

                                             cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat            >  1:498142/1‑69 (MQ=255)

                                             cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat            >  1:1851978/1‑69 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:148533/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:803712/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:775302/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:714515/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:559543/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:242033/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:1393703/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:2452634/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:2951010/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:2457302/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:2893267/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:2817377/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:216792/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:1919548/60‑1 (MQ=255)

                                              aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:173592/60‑1 (MQ=255)

                                              aCGTTGAGTCATCCGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:3183835/60‑1 (MQ=255)

                                               cGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:2398404/59‑1 (MQ=255)

                                                     gTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGc     <  1:991480/68‑1 (MQ=255)

                                                       cATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCtgt  <  1:540980/69‑1 (MQ=255)

                                                       cATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCtgt  <  1:2685292/69‑1 (MQ=255)

                                                           tGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc                    <  1:296950/47‑1 (MQ=255)

CTTCCATCCGCTGCTGGCTAACAATAGTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGT  >  minE/740533‑740656

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