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	1,690,476	T→C	45.8%	P382P (CCA→CCG)	hscA ←	DnaK‑like molecular chaperone specific for IscU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,690,476	0	T	C	45.8%	3.8 / 48.3	59	P382P (CCA→CCG)	hscA	DnaK‑like molecular chaperone specific for IscU
Reads supporting (aligned to +/- strand): ref base T (13/19); new base C (19/8); total (32/27)
Fisher's exact test for biased strand distribution p-value = 3.55e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

CATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGCGACGAC  >  minE/1690419‑1690529

cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                            <  1:2312864/69‑1 (MQ=255)

cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                            <  1:2865068/69‑1 (MQ=255)

cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                            <  1:1756529/69‑1 (MQ=255)

cATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                            <  1:123153/69‑1 (MQ=255)

 aTCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                            <  1:2281996/68‑1 (MQ=255)

 aTCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAcc                                            <  1:852163/68‑1 (MQ=255)

    gTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAccc                                           >  1:1007978/1‑66 (MQ=255)

    gTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAccc                                           >  1:3312450/1‑66 (MQ=255)

    gTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTAccc                                           >  1:604020/1‑66 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:645925/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:701922/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:1653558/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:1201769/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:760250/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:2723011/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:2514860/68‑1 (MQ=255)

         gAGGCCCAGCGACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGaa                                    <  1:819569/68‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:3294481/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:3273610/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:3199050/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:2337681/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:2317794/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:1010089/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:2131405/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:1707408/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:1786145/69‑1 (MQ=255)

                   gACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:1182647/69‑1 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAata                                  >  1:751751/1‑60 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:590288/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:488317/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:426950/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:1417889/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:1452255/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:137425/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:717512/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:1764025/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:2849937/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:2680290/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:1806149/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:956581/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:985099/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:2039060/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:2307900/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:2284396/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGCAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:2044506/1‑69 (MQ=255)

                   gACAGCGGGATCACATCCAGAAACAGCATTTCGCTGTCCGGCTTGTTACCCACCAGAATATCCGCCTGa                         >  1:1261635/1‑69 (MQ=255)

                    aCAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:2221740/68‑1 (MQ=255)

                    aCAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGa                         <  1:3136759/68‑1 (MQ=255)

                        tGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATcgc                    >  1:360649/1‑69 (MQ=255)

                        tGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATcgc                    >  1:3272479/1‑69 (MQ=255)

                              cacaTCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCTACCAGAATATCCGCCTGAATCGCCGCGcc              <  1:516232/69‑1 (MQ=255)

                                           aGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGCgacgac  >  1:1614133/1‑68 (MQ=255)

                                           aGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGCgacgac  >  1:112933/1‑68 (MQ=255)

                                           aGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGCgacgac  >  1:1819997/1‑68 (MQ=255)

                                           aGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGCgacgac  >  1:1886664/1‑68 (MQ=255)

                                                 tCGCTGTCTGGCTTGTTACCCACCAGAATATCCTCCTGAATCGCCGCGCCAATAGcgac     >  1:1714921/1‑59 (MQ=255)

                                                 tCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGcgac     >  1:592747/1‑59 (MQ=255)

                                                 tCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGcgac     >  1:284177/1‑59 (MQ=255)

                                                 tCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGcgac     >  1:1044568/1‑59 (MQ=255)

CATCGTTTCGAGGCCCAGCGACAGTGGGATCACATCAAGCAACAGCATTTCGCTGTCTGGCTTGTTACCCACCAGAATATCCGCCTGAATCGCCGCGCCAATAGCGACGAC  >  minE/1690419‑1690529

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