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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,946,407	G→A	57.1%	intergenic (‑121/+121)	fecI ← / ← dnaC	RNA polymerase, sigma 19 factor/DNA biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,946,407	0	G	A	57.1%	19.0 / 66.0	56	intergenic (‑121/+121)	fecI/dnaC	RNA polymerase, sigma 19 factor/DNA biosynthesis protein
Reads supporting (aligned to +/- strand): ref base G (8/16); new base A (18/14); total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-01

GGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGA  >  minE/2946337‑2946472

ggTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGtgttg                                                                   >  1:3274599/1‑71 (MQ=255)

         tACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggtagg                                                          >  1:2903315/1‑71 (MQ=255)

             aTTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggtagg                                                          <  1:3216644/67‑1 (MQ=255)

              ttGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTtata                                                                 <  1:2739968/59‑1 (MQ=255)

              ttGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATaa                                                     <  1:3094588/71‑1 (MQ=255)

              ttGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGtata                                                      >  1:2810337/1‑70 (MQ=255)

               tGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaa                                                     <  1:3059877/70‑1 (MQ=255)

                ggAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATaaaa                                                   >  1:1623539/1‑71 (MQ=255)

                 gAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAAt                                                  <  1:1240317/71‑1 (MQ=255)

                 gAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaaa                                                   <  1:698962/70‑1 (MQ=255)

                  aaaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATg                                                 <  1:2684205/71‑1 (MQ=255)

                   aaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATgg                                                >  1:2315891/1‑71 (MQ=255)

                     tAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGa                                              <  1:230107/71‑1 (MQ=255)

                      aaaaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGAt                                             >  1:1533957/1‑71 (MQ=255)

                       aaaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATg                                            <  1:2797801/71‑1 (MQ=255)

                        aaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATg                                            >  1:1105560/1‑70 (MQ=255)

                             tttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCct                                      >  1:645292/1‑71 (MQ=255)

                             tttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCct                                      <  1:24142/71‑1 (MQ=255)

                              ttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCctc                                     >  1:1255201/1‑71 (MQ=255)

                              ttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCctc                                     >  1:2435650/1‑71 (MQ=255)

                               tCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGTGATGGAGCctct                                    >  1:2643013/1‑71 (MQ=255)

                               tCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATg                                                 >  1:2349305/1‑58 (MQ=255)

                                ccAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggtaggt                                                         >  1:2936798/1‑49 (MQ=255)

                                  aaTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCt                                 <  1:3773147/71‑1 (MQ=255)

                                  aaTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCt                                 <  1:3226774/71‑1 (MQ=255)

                                   aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCtt                                >  1:147867/1‑71 (MQ=255)

                                   aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCt                                 <  1:2894796/70‑1 (MQ=255)

                                    tAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTc                               <  1:84879/71‑1 (MQ=255)

                                    tAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTc                               <  1:1028393/71‑1 (MQ=255)

                                    tAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTc                               >  1:2684174/1‑71 (MQ=255)

                                     aGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCt                              >  1:1347459/1‑71 (MQ=255)

                                     aGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCt                              >  1:2285217/1‑71 (MQ=255)

                                      gACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATgg                                                <  1:786987/52‑1 (MQ=255)

                                      gACATTTTTAACATGTTGTTTT‑‑TAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGc                           <  1:1460205/71‑1 (MQ=255)

                                        cATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGc                           <  1:2856363/71‑1 (MQ=255)

                                          tttttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAt                         <  1:3348145/71‑1 (MQ=255)

                                          tttttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAt                         <  1:3343716/71‑1 (MQ=255)

                                          tttttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGAt                                             <  1:3159714/51‑1 (MQ=255)

                                           ttttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTc                               <  1:1916190/64‑1 (MQ=255)

                                           ttttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtg                        >  1:932677/1‑71 (MQ=255)

                                           ttttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtg                        >  1:2676091/1‑71 (MQ=255)

                                             ttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtgt                       <  1:2064850/70‑1 (MQ=255)

                                             ttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGATTCTGGCAtgt                       <  1:1607877/70‑1 (MQ=255)

                                               aaCATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATgtgt                     <  1:2271023/70‑1 (MQ=255)

                                                     ttgttTTTCTAAGTGTTGTAAGGTAGGTATAAAATgg                                                <  1:1770959/37‑1 (MQ=255)

                                                     ttgttTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGa                                              >  1:2249314/1‑39 (MQ=255)

                                                       gttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGc                                        >  1:2447015/1‑43 (MQ=255)

                                                       gttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGc                                        >  1:1758073/1‑43 (MQ=255)

                                                       gttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCt                              >  1:2045949/1‑53 (MQ=255)

                                                       gttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGa             <  1:2158281/70‑1 (MQ=255)

                                                          tttCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGa         >  1:3907295/1‑71 (MQ=255)

                                                           ttCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGa         <  1:968961/70‑1 (MQ=255)

                                                             cTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGAc        >  1:1237585/1‑69 (MQ=255)

                                                               aaGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCt                              >  1:3379409/1‑45 (MQ=255)

                                                               aaGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAg              <  1:524675/61‑1 (MQ=255)

                                                                aGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGc                           <  1:1841929/47‑1 (MQ=255)

                                                                aGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCat    >  1:638653/1‑70 (MQ=255)

                                                                aGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCat    <  1:3020241/70‑1 (MQ=255)

                                                                      gtAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCatga  >  1:1905120/1‑66 (MQ=255)

GGTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGA  >  minE/2946337‑2946472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A