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	2,498,663	T→C	42.6%	A401A (GCT→GCC)	ilvB →	acetolactate synthase I, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,498,663	0	T	C	42.6%	11.9 / 39.6	54	A401A (GCT→GCC)	ilvB	acetolactate synthase I, large subunit
Reads supporting (aligned to +/- strand): ref base T (19/12); new base C (7/16); total (26/28)
Fisher's exact test for biased strand distribution p-value = 3.09e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.96e-01

CTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGTT  >  minE/2498597‑2498721

cTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTa                                                          >  1:1141094/1‑69 (MQ=255)

cTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTa                                                          <  1:3342673/69‑1 (MQ=255)

cTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTa                                                          >  1:323637/1‑69 (MQ=255)

cTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTa                                                          <  1:2076421/69‑1 (MQ=255)

cTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTa                                                          <  1:429952/69‑1 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:1179183/1‑69 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:1488751/1‑69 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:1180360/1‑69 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:297135/1‑69 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:2763560/1‑69 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:498126/1‑69 (MQ=255)

  gtgtCGATGACAATGCGATTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATc                                                        >  1:275021/1‑69 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGGATCAGATGTGGACCGCGCAAGCTTATCCGCTc                                                   >  1:1968724/1‑69 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCt                                                    >  1:2834901/1‑68 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTc                                                   >  1:652412/1‑69 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTc                                                   >  1:2658164/1‑69 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTc                                                   >  1:1291139/1‑69 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTc                                                   >  1:1562188/1‑69 (MQ=255)

       gATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTc                                                   >  1:598057/1‑69 (MQ=255)

                gCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATAGcc                                            >  1:1019774/1‑67 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCTCTCAATCGccc                                           <  1:204628/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCACTCGccc                                           <  1:3463/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:2693/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:2665709/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:3319656/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:3087664/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:3415227/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:2085378/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:373539/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:1975392/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:1917228/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:479309/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:533057/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:1578970/65‑1 (MQ=255)

                   aTTATCACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGCCTATCCGCTCAATCGccc                                           <  1:1577656/65‑1 (MQ=255)

                   aTTATAACCACCGACGTGGGTCAGCATCAGATGTGGACCGCGCAAGACTATCCGCTCAATCGccc                                           <  1:67214/65‑1 (MQ=255)

                     tATCACCACCGACGTTGGTCAGCATCTGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGcc                                      <  1:2051233/68‑1 (MQ=255)

                     tATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGcc                                      <  1:1321695/68‑1 (MQ=255)

                     tATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGcc                                      <  1:1613160/68‑1 (MQ=255)

                      aTCACCACTGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAg                                    >  1:2314814/1‑69 (MQ=255)

                      aTCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAg                                    >  1:217958/1‑69 (MQ=255)

                           ctccGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCGCAATCGCCCACGCCAGTGGCt                               <  1:383380/67‑1 (MQ=255)

                           caccGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCt                               <  1:39184/69‑1 (MQ=255)

                           caccGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCt                               <  1:1527736/69‑1 (MQ=255)

                                    tGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCgg                      >  1:251198/1‑69 (MQ=255)

                                    tGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCgg                      >  1:258777/1‑69 (MQ=255)

                                    tGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCgg                      >  1:3114867/1‑69 (MQ=255)

                                    tGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCgg                      >  1:3096622/1‑69 (MQ=255)

                                       tCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCa                                                  <  1:2973298/38‑1 (MQ=255)

                                                        ccGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGtt  >  1:2000162/1‑69 (MQ=255)

                                                        ccGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGtt  >  1:1885244/1‑69 (MQ=255)

                                                        ccGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGtt  >  1:144627/1‑69 (MQ=255)

                                                        ccGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGt   <  1:16237/68‑1 (MQ=255)

                                                        ccGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGt   <  1:1593155/68‑1 (MQ=255)

CTGTGTCGATGACAATGCAATTATCACCACCGACGTTGGTCAGCATCAGATGTGGACCGCGCAAGCTTATCCGCTCAATCGCCCACGCCAGTGGCTGACCTCCGGTGGGCTGGGCACGATGGGTT  >  minE/2498597‑2498721

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