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	771,851	C→A	45.0%	L12L (CTG→CTT)	hflD ←	predicted lysogenization regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	771,851	0	C	A	45.0%	18.9 / 57.6	60	L12L (CTG→CTT)	hflD	predicted lysogenization regulator
Reads supporting (aligned to +/- strand): ref base C (15/18); new base A (17/10); total (32/28)
Fisher's exact test for biased strand distribution p-value = 2.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.06e-01

ACAATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTCCTTG  >  minE/771794‑771902

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          <  1:1147361/69‑1 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          <  1:2559814/69‑1 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          >  1:2631659/1‑69 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          <  1:21982/69‑1 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          <  1:67754/69‑1 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          >  1:2747566/1‑69 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          >  1:2751565/1‑69 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          >  1:2832653/1‑69 (MQ=255)

acaATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAAGGt                                          <  1:3097660/69‑1 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          <  1:104128/68‑1 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGt                                          >  1:2071441/1‑68 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:424670/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:2574068/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:3174518/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:3249058/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:3322064/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:3036791/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:2886106/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:293926/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:1565995/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:756100/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:150413/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:1499827/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:834381/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:135663/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:877590/1‑69 (MQ=255)

 caATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTg                                         >  1:2946812/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:3011728/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:2031011/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:3299755/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:2027144/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:1903117/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:436128/1‑69 (MQ=255)

   aTGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:1060170/1‑69 (MQ=255)

   aTGCCCATGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGAt                                       >  1:440343/1‑69 (MQ=255)

     gCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGt                                     >  1:400646/1‑69 (MQ=255)

                                ggCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGt                                          <  1:1981563/37‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:3429390/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:955088/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:1172227/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:2418370/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:1518435/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:2299500/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:2215107/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:1654124/69‑1 (MQ=255)

                                 gCGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:1729703/69‑1 (MQ=255)

                                  cGTGCCGACTGACAAATACCGGCAAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGc         <  1:2868235/68‑1 (MQ=255)

                                    tGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:1748404/69‑1 (MQ=255)

                                    tGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:943450/69‑1 (MQ=255)

                                    tGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:1310937/69‑1 (MQ=255)

                                    tGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:2337661/69‑1 (MQ=255)

                                    tGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:3234953/69‑1 (MQ=255)

                                    tGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:2670370/69‑1 (MQ=255)

                                    ggCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTc      <  1:2861554/68‑1 (MQ=255)

                                      ccGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTCCt    >  1:2100390/1‑69 (MQ=255)

                                      ccGACTGACAAATACCGGCCAGGGCGAGGGTGATGTAATAGTAATTCTTTGCCACGTTCACTGCTTCCt    >  1:576063/1‑69 (MQ=255)

                                        gACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTCCTTg  <  1:189420/69‑1 (MQ=255)

                                        gACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTCCTTg  <  1:1380930/69‑1 (MQ=255)

                                                    ccGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGtt               <  1:1746687/44‑1 (MQ=255)

                                                    ccGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGtt               <  1:693014/44‑1 (MQ=255)

ACAATGCCCCTGGTGAGCGAGTTGTTGCACCAGGCGTGCCGACTGACAAATACCGGCCAGGGCGAGGGTGATGTCATAGTAATTCTTTGCCACGTTCACTGCTTCCTTG  >  minE/771794‑771902

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