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	1,683,726	C→T	59.4%	A416A (GCG→GCA)	yfhM ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,683,726	0	C	T	59.4%	21.7 / 42.7	63	A416A (GCG→GCA)	yfhM	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (12/13); new base T (16/21); total (29/34)
Fisher's exact test for biased strand distribution p-value = 7.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

AACGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATT  >  minE/1683660‑1683765

aaCGACGCTCCTGAGTACCTGCCCATCGTGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGc                                       <  1:2459179/69‑1 (MQ=255)

aaCGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGc                                       <  1:614646/69‑1 (MQ=255)

aaCGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGc                                       <  1:2653533/69‑1 (MQ=255)

aaCGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGc                                       <  1:694354/69‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:969753/67‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:2418070/67‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:2311864/67‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:460696/67‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:196901/67‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:606665/67‑1 (MQ=255)

   gacgCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCt                                      <  1:698084/67‑1 (MQ=255)

            gAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTg                            >  1:2429865/1‑68 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:3356685/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:336591/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:3335237/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:2826283/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:2928834/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:926350/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:3290775/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:2422457/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:3246325/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:2380464/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:212967/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:2038813/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:489777/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:1865500/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:177394/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:655386/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:1665748/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:952189/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:1457626/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:1348538/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGt                               <  1:1187174/50‑1 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCa                       >  1:2728039/1‑58 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:485662/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:556391/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:841929/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:3164124/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:724698/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:2673069/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:2669791/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:2669137/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:2365343/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:1974177/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:1851685/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:928296/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:935295/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACCGTCTGCATCACGCAGCAAAcc            >  1:1293189/1‑69 (MQ=255)

                           gggTTTAATCACGTCTAACTTGATGGGTTGATCGGGCAATGCTTTACAGTCTGCATCACGCAGGAAAcc            >  1:332482/1‑69 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:2755689/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:645717/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:636895/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:420240/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:3061600/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:111165/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:2597501/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:1693937/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:1648877/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:1127240/1‑68 (MQ=255)

                                tAATCACGTCTAACTTGATGGGTTGATTGGGCAAAGCTTTACCGTCTGCATCACGCAGCAAACCATTg        >  1:1622591/1‑68 (MQ=255)

                                   tCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAgg     <  1:581583/68‑1 (MQ=255)

                                     aCGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCa                       <  1:2648740/48‑1 (MQ=255)

                                     aCGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCCCGCAGCAAACCATTGAGGAtt  >  1:874393/1‑69 (MQ=255)

AACGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATT  >  minE/1683660‑1683765

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