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	2,785,369	G→A	36.1%	intergenic (‑29/‑183)	pepE ← / → yjbC	(alpha)‑aspartyl dipeptidase/23S rRNA pseudouridine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,785,369	0	G	A	36.1%	61.3 / 53.4	92	intergenic (‑29/‑183)	pepE/yjbC	(alpha)‑aspartyl dipeptidase/23S rRNA pseudouridine synthase
Reads supporting (aligned to +/- strand): ref base G (35/23); new base A (7/26); total (42/50)
Fisher's exact test for biased strand distribution p-value = 4.12e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

CGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCG  >  minE/2785314‑2785422

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:754565/1‑69 (MQ=255)

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:2881242/1‑69 (MQ=255)

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:28040/1‑69 (MQ=255)

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:1404784/1‑69 (MQ=255)

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:1821415/1‑69 (MQ=255)

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:1694289/1‑69 (MQ=255)

cGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCa                                          >  1:1596166/1‑69 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:1153526/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:923988/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:547865/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:3189562/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:2899697/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:2863566/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:2569793/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:2025733/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAAGCa                                                  >  1:256545/1‑60 (MQ=255)

 gAGTTACTCAATAAAAGCAGTTCCATTACTTCTACGGTTAGTAAGAAATCACGGGAGGCa                                                  >  1:2854424/1‑60 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:2623314/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:536579/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:435346/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:342175/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:712364/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:738501/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:2588043/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:1173568/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:2428312/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:2082435/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:1596985/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:902913/68‑1 (MQ=255)

     tACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:898188/68‑1 (MQ=255)

      aCTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:1309382/67‑1 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAAttt                                <  1:58811/67‑1 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAAttt                                <  1:2146274/67‑1 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAAttt                                <  1:3364338/67‑1 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:222204/1‑68 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:3197912/1‑68 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:2476939/1‑68 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:2140679/1‑68 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:2980364/1‑68 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:396744/1‑68 (MQ=255)

            tAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTa                               >  1:2939806/1‑68 (MQ=255)

             aaaaGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAAc                             <  1:1334038/69‑1 (MQ=255)

             aaaaGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAAc                             <  1:2744240/69‑1 (MQ=255)

                 gCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACt                         <  1:181585/69‑1 (MQ=255)

                 gCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACt                         <  1:1938312/69‑1 (MQ=255)

                       ccATTACTTCTCCGGTTATTAAGAAATCACGGCAGGc                                                   <  1:1587684/37‑1 (MQ=38)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:2582591/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:606509/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:3110762/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:1933908/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:1944875/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:2833082/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:2416821/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:2245571/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:610454/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:2110433/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGc                                                   <  1:617713/37‑1 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGa                   >  1:1248816/1‑69 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGa                   >  1:283254/1‑69 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGa                   >  1:279287/1‑69 (MQ=255)

                       ccATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGa                   >  1:1457854/1‑69 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:181432/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:879560/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:525080/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:570192/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:2024780/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:347342/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:19261/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:57587/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:2769243/69‑1 (MQ=255)

                           tACTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:1291568/69‑1 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACt                         >  1:3286308/1‑58 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACt                         >  1:828423/1‑58 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACt                         >  1:1956776/1‑58 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATgg              >  1:829811/1‑69 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATgg              >  1:1530167/1‑69 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATgg              >  1:2654337/1‑69 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATgg              >  1:1987999/1‑69 (MQ=255)

                            aCTTCTCCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGCGAATTTAACCACTTACTGACATg               <  1:1505747/68‑1 (MQ=255)

                                 tcCGGTTAGTAAGAAAACACGGAAGGAATGCTACCACTGc                                      <  1:1419786/40‑1 (MQ=255)

                                       tAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCAc         <  1:3155152/63‑1 (MQ=255)

                                       tAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCAc         <  1:3033807/63‑1 (MQ=255)

                                       tAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCAc         <  1:2153913/63‑1 (MQ=255)

                                       tAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCAc         <  1:110267/63‑1 (MQ=255)

                                       tAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGt    >  1:2868257/1‑68 (MQ=255)

                                       tAGTAAGAAATCACGGGAGGCATGCTACCACCGCGAATTTAACCACTTACTGACATGGCTCAc         <  1:476644/63‑1 (MQ=255)

                                        aGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCg  >  1:1228954/1‑69 (MQ=255)

                                        aGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCg  >  1:3172122/1‑69 (MQ=255)

                                        aGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCg  >  1:3162397/1‑69 (MQ=255)

                                        aGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCg  >  1:1281604/1‑69 (MQ=255)

                                        aGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCg  >  1:1429317/1‑69 (MQ=255)

                                        aGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCg  >  1:1982243/1‑69 (MQ=255)

CGAGTTACTCAATAAAAGCAGTTCCATTACTTCTCCGGTTAGTAAGAAATCACGGGAGGCATGCTACCACTGCGAATTTAACCACTTACTGACATGGCTCACGATGTCG  >  minE/2785314‑2785422

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A