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	2,392,429	C→T	38.5%	V107V (GTG→GTA)	recQ ←	ATP‑dependent DNA helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,392,429	0	C	T	38.5%	29.3 / 34.6	57	V107V (GTG→GTA)	recQ	ATP‑dependent DNA helicase
Reads supporting (aligned to +/- strand): ref base C (24/11); new base T (13/9); total (37/20)
Fisher's exact test for biased strand distribution p-value = 5.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCATCAGGCGTTCCGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCAG  >  minE/2392368‑2392497

gCATCAGGCGTTCCGGGGCGATATAAAGCAGACGAATTTGCCCTGTGCGGCAGCCTGTCATCACTTCa                                                                <  1:2667319/68‑1 (MQ=255)

gCATCAGGCGTTCCGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCa                                                                <  1:1374844/68‑1 (MQ=255)

  aTCAGGCGTTCCGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGt                                                             <  1:1898191/69‑1 (MQ=255)

            ccGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGtt                                                            >  1:103139/1‑60 (MQ=255)

            ccGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTcgc                                                   >  1:1839030/1‑69 (MQ=255)

            ccGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTcg                                                    >  1:1438693/1‑68 (MQ=255)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:2297142/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:2216265/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:2469293/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:1709328/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:533546/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:625862/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:850148/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:125194/44‑1 (MQ=37)

                       taAAGCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTc                                                                 <  1:1051625/44‑1 (MQ=37)

                       taAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTg                                                        <  1:3291360/53‑1 (MQ=255)

                       taAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTg                                                        <  1:3150245/53‑1 (MQ=255)

                       taAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTg                                                        <  1:1027922/53‑1 (MQ=255)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:446186/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:3272475/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:2834064/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:915762/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:2637894/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:2300373/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:932623/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:2073011/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:1199863/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:1549638/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:166365/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:1663919/1‑43 (MQ=37)

                           gCAGGCGGATTTGCCCGGTGCGGCAGCCTGTCATTACTTCAAgc                                                             >  1:1773536/1‑43 (MQ=37)

                            cAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGa                                      >  1:2872380/1‑66 (MQ=255)

                            cAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAg                                     >  1:2780692/1‑67 (MQ=255)

                            cAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAg                                     >  1:3283738/1‑67 (MQ=255)

                            cAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAg                                     >  1:3048752/1‑67 (MQ=255)

                                           ggTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCAcgccgccgc                    <  1:842343/69‑1 (MQ=255)

                                           ggTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCAcgccgccgc                    <  1:3436380/69‑1 (MQ=255)

                                           ggTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCAcgccgccgc                    <  1:3416459/69‑1 (MQ=255)

                                           ggTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCAcgccgccgc                    <  1:2874389/69‑1 (MQ=255)

                                           ggTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCAcgccgccgc                    <  1:243827/69‑1 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCa                  >  1:1552375/1‑68 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:2613751/1‑69 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:2269798/1‑69 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:345405/1‑69 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:2382050/1‑69 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:2773619/1‑69 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:2026672/1‑69 (MQ=255)

                                              gCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCAc                 >  1:321252/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCAcgccgcc                      >  1:2850610/1‑55 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:1186155/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:1693645/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:3301116/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:2802980/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:2513814/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:2346753/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:1533905/1‑69 (MQ=255)

                                                       tGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGc        >  1:1504806/1‑69 (MQ=255)

                                                             caCTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCa   >  1:346887/1‑68 (MQ=255)

                                                             caCTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCAg  >  1:2000842/1‑69 (MQ=255)

                                                             caCTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCAg  >  1:1421468/1‑69 (MQ=255)

                                                             caCTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCAg  >  1:350562/1‑69 (MQ=255)

                                                             caCTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCAg  >  1:3178517/1‑69 (MQ=255)

GCATCAGGCGTTCCGGGGCGATATAAAGCAGACGAATTTGCCCGGTGCGGCAGCCTGTCATCACTTCAAGTTGCTGTTCGCGGGTTTGCGTCGAGTTAAGGCACGCCGCCGCCACGCCGTTGGCTTGCAG  >  minE/2392368‑2392497

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