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	383,199	T→C	32.2%	T203T (ACT→ACC)	entB →	isochorismatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	383,199	0	T	C	32.2%	50.0 / 32.4	65	T203T (ACT→ACC)	entB	isochorismatase
Reads supporting (aligned to +/- strand): ref base T (15/29); new base C (9/12); total (24/41)
Fisher's exact test for biased strand distribution p-value = 5.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

CCGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTGATCCTGCCG  >  minE/383136‑383262

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:241062/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:1056975/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:534253/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:3269726/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:837224/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:1505636/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:1466331/68‑1 (MQ=255)

ccGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTgaag                                                             <  1:1443666/68‑1 (MQ=255)

     aCGAGCATTTGATGTCTCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTAc                                                       <  1:1626493/69‑1 (MQ=255)

     aCGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTAc                                                       >  1:189243/1‑69 (MQ=255)

     aCGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTAc                                                       <  1:2968321/69‑1 (MQ=255)

     aCGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTAc                                                       <  1:1287238/69‑1 (MQ=255)

     aCGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTAc                                                       <  1:120679/69‑1 (MQ=255)

      cGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTAc                                                       <  1:2704832/68‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:2718425/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:563857/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:2611146/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:2815483/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:543689/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:2914172/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:2925502/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:473388/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:3342233/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:3364581/69‑1 (MQ=255)

        aGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:1068202/69‑1 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:3189349/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:3216993/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:3406174/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:2122714/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:1264764/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:899095/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:223125/1‑68 (MQ=255)

              tGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCa                                               >  1:1654657/1‑68 (MQ=255)

                   tCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAg                                                 <  1:1589192/61‑1 (MQ=255)

                   tCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAg                                                 <  1:3331056/61‑1 (MQ=255)

                   tCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAg                                                 <  1:1270687/61‑1 (MQ=255)

                   tCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAg                                                 <  1:209485/61‑1 (MQ=255)

                   tCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAg                                                 <  1:2463157/61‑1 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:2771450/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:1745117/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:1955091/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:1114048/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:3005018/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:3141362/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:1514233/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:3362777/1‑69 (MQ=255)

                                   ccGGACGTTCTGGTCGGGTGGTGATGACCGAAGAATTGCTGCCAGCACCTATCCCCGCCAGCAAAgcgg                         >  1:1168521/1‑69 (MQ=255)

                                    cGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAgcggc                        <  1:1943673/69‑1 (MQ=255)

                                    cGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAgcggc                        <  1:448800/69‑1 (MQ=255)

                                    cGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAgcggc                        <  1:2061625/69‑1 (MQ=255)

                                    cGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAgcggc                        <  1:778011/69‑1 (MQ=255)

                                      gACGTTCTGGTCGGGTGGTGATGACCGAAGAATtgctgc                                                    <  1:2412802/39‑1 (MQ=37)

                                          ttCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGc                   >  1:951206/1‑68 (MQ=255)

                                          ttCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGc                   >  1:2410460/1‑68 (MQ=255)

                                          ttCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGc                   >  1:1376368/1‑68 (MQ=255)

                                          ttCTGGCAGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGc                   >  1:2025358/1‑68 (MQ=255)

                                            cTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTg                <  1:2017540/69‑1 (MQ=255)

                                                 cGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTg           <  1:3294060/69‑1 (MQ=255)

                                                 cGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTg           <  1:2503962/69‑1 (MQ=255)

                                                 cGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTg           <  1:795536/69‑1 (MQ=255)

                                                 cGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTg           <  1:157902/69‑1 (MQ=255)

                                                 cGGGTGGTGATGACTGAAGAATTACAGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTg           <  1:564540/69‑1 (MQ=255)

                                                  gggTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTGa          <  1:108075/69‑1 (MQ=255)

                                                          atgaCTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTGATCCTGCCg  >  1:326924/1‑69 (MQ=255)

                                                          atgaCTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTGATCCTGCCg  >  1:641324/1‑69 (MQ=255)

CCGTGACGAGCATTTGATGTCGCTGAAATATGTGGCCGGACGTTCTGGCCGGGTGGTGATGACTGAAGAATTACTGCCAGCACCTATCCCCGCCAGCAAAGCGGCGCTGCGTGAGGTGATCCTGCCG  >  minE/383136‑383262

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A