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	2,460,071	C→T	43.5%	P45S (CCT→TCT)	mioC →	FMN‑binding protein MioC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,460,071	0	C	T	43.5%	22.9 / 58.5	78	P45S (CCT→TCT)	mioC	FMN‑binding protein MioC
Reads supporting (aligned to +/- strand): ref base C (32/12); new base T (16/18); total (48/30)
Fisher's exact test for biased strand distribution p-value = 3.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01

CTGGAAGAGGCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAACCTTTC  >  minE/2460014‑2460138

cTGGAAGAGGCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          <  1:1072327/69‑1 (MQ=255)

cTGGAAGAGGCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          <  1:1235290/69‑1 (MQ=255)

cTGGAAGAGGCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          <  1:794282/69‑1 (MQ=255)

cTGGAAGAGGCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          <  1:488111/69‑1 (MQ=255)

         gCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATctggctg                                                 >  1:3271272/1‑69 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:216380/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:1012700/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:2194494/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:229348/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:1394532/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:1945088/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:1903086/1‑58 (MQ=255)

           gggTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAggg                                                          >  1:1520518/1‑58 (MQ=255)

               ttaaccaccGAAACGCTGCACGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATc                                           <  1:103579/66‑1 (MQ=255)

                     accGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTc                                      <  1:1806349/68‑1 (MQ=255)

                     accGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTc                                      <  1:785043/68‑1 (MQ=255)

                     accGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTc                                      <  1:2671143/68‑1 (MQ=255)

                     accGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTc                                      <  1:1421007/68‑1 (MQ=255)

                     accGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTc                                      <  1:2482238/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:2727910/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:370396/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:508620/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:3023412/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:564386/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:252808/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:597756/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:329879/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:3423160/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:2184651/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:2188496/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:2034629/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:1969910/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:1582226/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:1647397/68‑1 (MQ=255)

                                   cGGTCCGCTGTTGGAAGATCTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:335690/68‑1 (MQ=255)

                                   cGGTCCGCAGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCAGCTCAACCCACGGTGCCg                        <  1:1815621/68‑1 (MQ=255)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGTGGATCTGGCTGGTTATCa                                          >  1:1201062/1‑49 (MQ=255)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGtt                                              >  1:2090618/1‑45 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:3402655/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:3422513/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:368019/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:3114574/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:835257/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:2771431/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:2713680/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:1701365/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:712686/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:2151655/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:640735/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:2271351/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTATCa                                          >  1:712068/1‑49 (MQ=38)

                                    ggTCCGCTGTTGGAAGATTTATCTGCCTCGGGGATCTGGCTGGTTACCa                                          >  1:1457571/1‑49 (MQ=37)

                                       ccGCTGTTAGAAGATTTACCTGCCACAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGgaga                    <  1:2580758/68‑1 (MQ=255)

                                             ttAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTc                                      <  1:88701/44‑1 (MQ=255)

                                              tAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCg             >  1:581947/1‑68 (MQ=255)

                                              tAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCg             >  1:2930548/1‑68 (MQ=255)

                                              tAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCg             >  1:1382401/1‑68 (MQ=255)

                                               agaagaTTTACCTTCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:97500/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:2481422/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:1470569/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:1807040/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:2161013/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:2699147/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:280796/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:3307243/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCgg            >  1:3398232/1‑68 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCg             >  1:2463078/1‑67 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCg             >  1:3129765/1‑67 (MQ=255)

                                               agaagaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACACACGGTGCCGGAGATATTCCgg            >  1:2092786/1‑68 (MQ=255)

                                                   gaTTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAc       <  1:2284836/69‑1 (MQ=255)

                                                      ttACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctt    >  1:846657/1‑69 (MQ=255)

                                                      ttACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctt    >  1:2529484/1‑69 (MQ=255)

                                                      ttACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctt    >  1:671422/1‑69 (MQ=255)

                                                      ttACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctt    >  1:1670049/1‑69 (MQ=255)

                                                        aCCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGat                   >  1:1065190/1‑52 (MQ=255)

                                                        aCCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctttc  >  1:2922818/1‑69 (MQ=255)

                                                        aCCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctttc  >  1:1454220/1‑69 (MQ=255)

                                                        aCCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAAcctttc  >  1:3310688/1‑69 (MQ=255)

CTGGAAGAGGCGGGTTTTACCACCGAAACGCTGCACGGTCCGCTGTTAGAAGATTTACCTGCCTCAGGGATCTGGCTGGTTATCAGCTCCACCCACGGTGCCGGAGATATTCCGGACAACCTTTC  >  minE/2460014‑2460138

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