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	1,326,078	T→C	39.3%	V311V (GTA→GTG)	wcaK ←	predicted pyruvyl transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,326,078	0	T	C	39.3%	26.0 / 40.1	61	V311V (GTA→GTG)	wcaK	predicted pyruvyl transferase
Reads supporting (aligned to +/- strand): ref base T (17/20); new base C (8/16); total (25/36)
Fisher's exact test for biased strand distribution p-value = 4.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.41e-01

TACCGACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGGTCGTCTTT  >  minE/1326011‑1326143

tACCGACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTa                                                                  <  1:2100385/69‑1 (MQ=255)

tACCGACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTa                                                                  <  1:1820560/69‑1 (MQ=255)

tACCGACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTa                                                                  <  1:3413799/69‑1 (MQ=255)

tACCGACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTa                                                                  <  1:1692206/69‑1 (MQ=255)

    gACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGt                                                               >  1:3097797/1‑68 (MQ=255)

    gACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGt                                                               >  1:1716116/1‑68 (MQ=255)

    gACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTACAGATCGTTGAGTTCATCCATCACTACg                                                                >  1:780951/1‑67 (MQ=255)

               cacaGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAg                                                   >  1:1040514/1‑69 (MQ=255)

               cacaGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAg                                                   >  1:115029/1‑69 (MQ=255)

               cacaGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAg                                                   >  1:2098929/1‑69 (MQ=255)

               cacaGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAg                                                   >  1:1773171/1‑69 (MQ=255)

               cacaGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAg                                                   >  1:344189/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAgg                                                  >  1:3411498/1‑68 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:2584421/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:2678427/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:1904202/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:3376463/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:324755/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:2154873/1‑69 (MQ=255)

                 caGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACTGGCAGGa                                                 >  1:354866/1‑69 (MQ=255)

                   ggCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATc                                               >  1:581954/1‑69 (MQ=255)

                   ggCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATc                                               >  1:2454539/1‑69 (MQ=255)

                   ggCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATc                                               >  1:2358183/1‑69 (MQ=255)

                   ggCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATc                                               >  1:2263480/1‑69 (MQ=255)

                   ggCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATc                                               >  1:2756117/1‑69 (MQ=255)

                   ggCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATc                                               >  1:1106398/1‑69 (MQ=255)

                      ccccAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCt                                            <  1:1224084/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:614960/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:3153566/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:321228/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:843287/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:264195/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:444811/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:432367/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:2351789/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:2125686/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:1217851/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:135765/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:1700137/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:2120077/69‑1 (MQ=255)

                             aTTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:1954030/69‑1 (MQ=255)

                              ttttGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCt                                    <  1:1000467/69‑1 (MQ=255)

                              ttttGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCt                                    <  1:1100925/69‑1 (MQ=255)

                              ttttGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCt                                    <  1:1851164/69‑1 (MQ=255)

                              ttttGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCt                                    <  1:3271779/69‑1 (MQ=255)

                              ttttGCCCATTTCCAGATCGTTGAGTTCATCCATCACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:2911411/68‑1 (MQ=255)

                                         tCCAGATCGTTGAGTTCATCCATCACTACGTGGAAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTg                         >  1:1265959/1‑69 (MQ=255)

                                                 gTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGccac                 <  1:3032075/69‑1 (MQ=255)

                                                 gTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGccac                 <  1:2794606/69‑1 (MQ=255)

                                                 gTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGccac                 <  1:2413104/69‑1 (MQ=255)

                                                          atccatcACCACGTGGTAACGGGCAGGATCGCTGATGTGc                                     <  1:2344464/40‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:1995769/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:196062/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:311361/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:1777296/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:1481206/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:50275/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:518383/68‑1 (MQ=255)

                                                           tccatcACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGgtc        <  1:1119769/68‑1 (MQ=255)

                                                                 aCTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGGTCGTCttt  >  1:2005354/1‑68 (MQ=255)

                                                                 aCTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGGTCGTCttt  >  1:3137618/1‑68 (MQ=255)

TACCGACGGTGAGTTCACAGGCCCCCAGAATTTTGCCCATTTCCAGATCGTTGAGTTCATCCATCACTACGTGGTAACGGGCAGGATCGCTGATGTGCTGGCGCAGGTTGAGCGCCACCATGCGGTCGTCTTT  >  minE/1326011‑1326143

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