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 F8 I0 R2	296	77.6	4260404	88.1%	3753415	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,987,375	A→G	55.8%	A48A (GCA→GCG)	yjtD →	predicted rRNA methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,987,375	0	A	G	55.8%	20.0 / 66.3	52	A48A (GCA→GCG)	yjtD	predicted rRNA methyltransferase
Reads supporting (aligned to +/- strand): ref base A (11/12); new base G (6/23); total (17/35)
Fisher's exact test for biased strand distribution p-value = 7.26e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.91e-01

CGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGTTACACGAT  >  minE/2987305‑2987441

cGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGca                                                                    <  1:938136/71‑1 (MQ=255)

cGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGca                                                                    <  1:334618/71‑1 (MQ=255)

cGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGca                                                                    <  1:3958997/71‑1 (MQ=255)

cGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGca                                                                    <  1:799155/71‑1 (MQ=255)

     gggTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATgt                                                               <  1:3847599/71‑2 (MQ=255)

     gggTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATgg                                                               <  1:2995660/71‑1 (MQ=255)

      ggTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGa                                                              <  1:161749/71‑1 (MQ=255)

        tttAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGcaca                                                                  >  1:2785246/1‑65 (MQ=255)

        tttAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGcaca                                                                  >  1:2425298/1‑65 (MQ=255)

          tAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGcgca                                                                  >  1:2229696/1‑63 (MQ=255)

          tAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGcaca                                                                  <  1:1330211/63‑1 (MQ=255)

          tAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGcaca                                                                  <  1:449887/63‑1 (MQ=255)

           aGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGcaca                                                                  <  1:3353995/62‑1 (MQ=255)

           aGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTg                                                          <  1:4120256/70‑1 (MQ=255)

                tCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGa                                                      >  1:2140511/1‑69 (MQ=255)

                tCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGa                                                      >  1:2687737/1‑69 (MQ=255)

                tCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGa                                                      >  1:2135403/1‑69 (MQ=255)

                tCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGa                                                      >  1:90424/1‑69 (MQ=255)

                tCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCAGCTGGGTCGCACATGGATCTGGTGa                                                      >  1:3922946/1‑69 (MQ=255)

                    cGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGa                                                      <  1:2102966/65‑1 (MQ=255)

                        ttGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGat                                            <  1:127653/71‑1 (MQ=255)

                        ttGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGat                                            <  1:3282473/71‑1 (MQ=255)

                        ttGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGa                                             >  1:110735/1‑70 (MQ=255)

                          gTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGata                                           <  1:1743055/70‑1 (MQ=255)

                          gTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGata                                           <  1:3050313/70‑1 (MQ=255)

                           tCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGataa                                          <  1:195564/70‑1 (MQ=255)

                           tCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGataa                                          <  1:3408967/70‑1 (MQ=255)

                                    aGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGtt                                >  1:2033564/1‑71 (MQ=255)

                                    aGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGtt                                >  1:3097636/1‑71 (MQ=255)

                                      gCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGt                                 <  1:840502/68‑1 (MQ=255)

                                      gCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGt                                 <  1:1139391/68‑1 (MQ=255)

                                      gCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGt                                 <  1:1623854/68‑1 (MQ=255)

                                       cacaCCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTc                             <  1:4030439/71‑1 (MQ=255)

                                        acacCTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTc                             <  1:87918/70‑1 (MQ=255)

                                        acacCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGttt                               >  1:999177/1‑68 (MQ=255)

                                         cacCTGGAGCCAGCCACCCGCTGGGTCGCGCATgg                                                               <  1:2876689/35‑1 (MQ=255)

                                         cacCTGGAGCCAGCCACCCGCTGGGTCGCGCATgg                                                               <  1:3252201/35‑1 (MQ=255)

                                         cacCTGGAGCCAGCCACCCGCTGGGTCGCGCATgg                                                               <  1:1663966/35‑1 (MQ=255)

                                            cTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGttt                               <  1:3651000/64‑1 (MQ=255)

                                            cTGGAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGAc                        <  1:1462746/71‑1 (MQ=255)

                                            cTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGAc                        <  1:1466407/71‑1 (MQ=255)

                                             tGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGAc                        >  1:1414353/1‑70 (MQ=255)

                                              ggAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTc                             >  1:1053612/1‑64 (MQ=255)

                                              ggAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTc                             >  1:1104312/1‑64 (MQ=255)

                                              ggAGCCAGCCACCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTc                             >  1:3938323/1‑64 (MQ=255)

                                                     gccaCCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTg                >  1:2291964/1‑70 (MQ=255)

                                                     gccaCCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTg                >  1:4170073/1‑70 (MQ=255)

                                                     gccaCCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGa               <  1:1784938/71‑1 (MQ=255)

                                                       caCCCGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAAt             >  1:1768466/1‑71 (MQ=255)

                                                       caCCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAtt                     <  1:3794391/63‑1 (MQ=255)

                                                       caCCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAtt                     <  1:1165552/63‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATCTTATTGATAATATTAAAGTTTTccc                           <  1:896601/55‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTccc                           <  1:2531674/55‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAt                      <  1:2277227/60‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAt                      <  1:2272216/60‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAt                      <  1:3177468/60‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAt                      <  1:1097249/60‑1 (MQ=255)

                                                         cccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAt                      <  1:19219/60‑1 (MQ=255)

                                                          ccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGt          <  1:4168786/71‑1 (MQ=255)

                                                          ccGCTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGt          <  1:1542413/71‑1 (MQ=255)

                                                             cTGGGTCGCGCATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACAt                      <  1:752703/56‑1 (MQ=255)

                                                                  tCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGTTACACGAt  >  1:122624/1‑71 (MQ=255)

CGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGTTACACGAT  >  minE/2987305‑2987441

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