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	1,882,657	A→G	52.2%	H159H (CAT→CAC)	relA ←	(p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,882,657	0	A	G	52.2%	6.9 / 81.5	94	H159H (CAT→CAC)	relA	(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand): ref base A (16/29); new base G (33/16); total (49/45)
Fisher's exact test for biased strand distribution p-value = 3.59e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.37e-01

GTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCAT  >  minE/1882594‑1882710

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:2821369/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:1144364/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:270179/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:585271/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:416966/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:1420889/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:316417/69‑1 (MQ=255)

gTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:1539885/69‑1 (MQ=255)

 ttGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:662094/68‑1 (MQ=255)

 ttGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGc                                                  <  1:2961875/68‑1 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2117924/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:256301/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2403728/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2395103/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2994645/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2075896/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2071847/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:2957808/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1047297/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:3045006/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:3120332/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:3413378/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:823207/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:865391/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1967516/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1639414/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1692403/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1499181/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1831716/1‑69 (MQ=255)

  tGGTGCACTCTTTTGCCGCCAGTACGCGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCaa                                                >  1:1408440/1‑69 (MQ=255)

   ggTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:2330417/68‑1 (MQ=255)

   ggTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:2827070/68‑1 (MQ=255)

   ggTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:2697463/68‑1 (MQ=255)

   ggTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:3032996/68‑1 (MQ=255)

   ggTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:2177963/68‑1 (MQ=255)

   ggTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:2145369/68‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:616945/69‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:2645763/69‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:2460150/69‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:2998861/69‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:3304077/69‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:900311/69‑1 (MQ=255)

       cacTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGc                                           <  1:1572796/69‑1 (MQ=255)

         ctctTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATTAGCAATACGCTc                                         >  1:2682289/1‑69 (MQ=255)

         ctctTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCt                                          >  1:2854429/1‑68 (MQ=255)

         ctctTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTc                                         >  1:1929223/1‑69 (MQ=255)

         ctctTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTc                                         >  1:2122239/1‑69 (MQ=255)

         ctctTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTc                                         >  1:2507911/1‑69 (MQ=255)

                          cacGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTtg                               >  1:2267544/1‑62 (MQ=255)

                          cacGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTtg                               >  1:791698/1‑62 (MQ=255)

                          cacGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTtg                               >  1:24972/1‑62 (MQ=255)

                          cacGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTtg                               <  1:1539490/62‑1 (MQ=255)

                           acGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTtg                               <  1:501018/61‑1 (MQ=255)

                              ttCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCa                    <  1:1707587/69‑1 (MQ=255)

                              ttCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCa                    <  1:1037158/69‑1 (MQ=255)

                              ttCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCa                    <  1:467521/69‑1 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCa                                                 >  1:3059651/1‑38 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcg                                        >  1:1172018/1‑46 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:2970368/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:998618/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:357341/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:488277/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:1576738/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:1734953/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTcc                                        >  1:1935219/1‑47 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTc                                         >  1:2346894/1‑46 (MQ=255)

                                cATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCaa                                                <  1:2593842/39‑1 (MQ=255)

                                      ccGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAat            >  1:2856987/1‑69 (MQ=255)

                                      ccGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAat            >  1:1454363/1‑69 (MQ=255)

                                      ccGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAat            >  1:1466667/1‑69 (MQ=255)

                                               cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc     >  1:2630309/1‑67 (MQ=255)

                                               cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc     >  1:2878482/1‑67 (MQ=255)

                                               cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc     >  1:1983126/1‑67 (MQ=255)

                                               cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc     >  1:1987240/1‑67 (MQ=255)

                                               cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc     >  1:2200071/1‑67 (MQ=255)

                                                ttttACTTCGCGCAGATGAGCAATACGCTCCGCCa                                    >  1:1967615/1‑35 (MQ=255)

                                                ttttACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCAt  >  1:1287920/1‑69 (MQ=255)

                                                ttttACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCAt  >  1:177736/1‑69 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2315389/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:3359949/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:3102358/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2207241/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:3090946/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2196941/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2178268/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2132390/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:1274307/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:704763/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:1521358/65‑1 (MQ=255)

                                                    aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2022466/65‑1 (MQ=255)

                                                    aCTTCGCGCACGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:3022766/65‑1 (MQ=255)

                                                    aCTTCGCCCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:2078308/65‑1 (MQ=255)

                                                     cTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt  <  1:3357073/64‑1 (MQ=255)

                                                           gcAGGTGAGCAATACGCTCCGCCTGTTTGATGACCACGCACCGAAAATCATCGACCAt  <  1:2365965/58‑1 (MQ=255)

GTTGGTACACTCTTTTGCCGCCAGTACACGTTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCAT  >  minE/1882594‑1882710

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