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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,259,808 C→T 23.7% A372A (GCG→GCA)  torZ ← trimethylamine N‑oxide reductase system III, catalytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,259,8080CT23.7% 136.6 / 38.8 76A372A (GCG→GCA) torZtrimethylamine N‑oxide reductase system III, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base C (30/28);  new base T (13/5);  total (43/33)
Fisher's exact test for biased strand distribution p-value = 1.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

GAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATC  >  minE/1259749‑1259877
                                                           |                                                                     
gAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCAc                                                            <  1:3032831/71‑1 (MQ=255)
gAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCAc                                                            <  1:2844667/71‑1 (MQ=255)
 aGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCAc                                                            >  1:4600250/1‑70 (MQ=255)
   aaaTGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGc                                                                 <  1:3618007/62‑1 (MQ=255)
   aaaTGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGAcga                                                          <  1:419678/69‑3 (MQ=255)
        gtAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATcc                                                    <  1:138006/70‑1 (MQ=255)
        gtAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATcc                                                    <  1:4525914/70‑1 (MQ=255)
         tAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATc                                                     >  1:3898621/1‑69 (MQ=255)
            gagaAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGc                                                        <  1:1149535/63‑1 (MQ=255)
            gagaAACCAAAACCGCCGCACGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGc                                                        <  1:248870/63‑1 (MQ=255)
              gaAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGtt                                              >  1:2201941/1‑71 (MQ=255)
               agaCCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCa                                                   >  1:402649/3‑65 (MQ=255)
                gaCCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGtttt                                            >  1:4128930/2‑70 (MQ=255)
                aaCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGc                                                                 <  1:3615561/50‑1 (MQ=255)
                aaCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCa                                                       <  1:908069/60‑1 (MQ=255)
                aaCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTc                                            <  1:2122035/71‑1 (MQ=255)
                 aCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTc                                            >  1:2733240/1‑70 (MQ=255)
                  ccAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCa                                                          >  1:2902326/1‑55 (MQ=255)
                   cAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGtttt                                            >  1:3137196/1‑67 (MQ=255)
                   cAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATcc                                                    <  1:1660741/60‑1 (MQ=255)
                   cAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgt                                                 <  1:3178490/63‑1 (MQ=255)
                      aaCCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCa                                      >  1:5384322/1‑71 (MQ=255)
                      aaCCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCa                                      >  1:2015270/1‑71 (MQ=255)
                         cgccgcCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGt                                         <  1:317868/65‑1 (MQ=255)
                          gccgccGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCa                                   >  1:2928180/1‑70 (MQ=255)
                          gccgccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCa                                   >  1:3376499/1‑70 (MQ=255)
                            cgccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTg                                          <  1:5535675/61‑1 (MQ=255)
                             gccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGttt                                             <  1:2246028/57‑1 (MQ=255)
                             gccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATAtt                               <  1:4789950/71‑1 (MQ=255)
                              ccgggTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCa                                      >  1:3004314/4‑63 (MQ=255)
                              cccGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTg                              >  1:2805669/1‑71 (MQ=255)
                                cGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGGATCCAGTGTTTCTGTTCACCATATTGCt                            <  1:3908737/71‑1 (MQ=255)
                                cGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAg                                                  >  1:1119392/1‑49 (MQ=255)
                                   tgtACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGgc                         >  1:2667483/1‑71 (MQ=255)
                                     tACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTg                                          <  1:3432571/52‑1 (MQ=255)
                                     tACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTg                                          <  1:1224449/52‑1 (MQ=255)
                                       ccAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgtgt                                               >  1:1547495/1‑45 (MQ=255)
                                       ccAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgtgt                                               >  1:2839865/1‑45 (MQ=255)
                                       ccAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgtgt                                               >  1:2318236/1‑45 (MQ=255)
                                           tttGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCAt                  >  1:4054543/3‑70 (MQ=255)
                                           tttGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCAt                  >  1:1989388/3‑70 (MQ=255)
                                           tCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCt                            <  1:148507/60‑1 (MQ=255)
                                            cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc                >  1:761480/1‑71 (MQ=255)
                                            cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc                >  1:4127653/1‑71 (MQ=255)
                                            cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc                >  1:3686733/1‑71 (MQ=255)
                                             tGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGtt                                        >  1:402258/1‑46 (MQ=255)
                                             tGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGtt                                        >  1:4328969/1‑46 (MQ=255)
                                             tGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGtt                                        >  1:3432523/1‑46 (MQ=255)
                                             tGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcc               >  1:5063077/1‑71 (MQ=255)
                                               cccTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcccc             <  1:2038243/71‑1 (MQ=255)
                                               cccTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcccc             <  1:4124712/71‑1 (MQ=255)
                                                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTccc              >  1:175182/4‑69 (MQ=255)
                                                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTccc              >  1:1510680/4‑69 (MQ=255)
                                                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTGGCGCTGCATTccc              >  1:5694394/4‑69 (MQ=255)
                                                cccaaCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCAACAAACTGTTGGCGCTGCATTCCCCa            <  1:5584119/68‑1 (MQ=255)
                                                ccTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTcccc             <  1:3988489/70‑1 (MQ=255)
                                                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGtt                                              <  1:5567807/35‑1 (MQ=255)
                                                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCAc                                     <  1:1748286/44‑1 (MQ=255)
                                                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCatat                                <  1:3359860/49‑1 (MQ=255)
                                                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCt                      <  1:1665276/59‑1 (MQ=255)
                                                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTccc              >  1:3949943/1‑67 (MQ=255)
                                                  tAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGc          >  1:3334757/1‑71 (MQ=255)
                                                   aaCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGcc         >  1:1835596/1‑71 (MQ=255)
                                                    aCATTGCTGCCAGCGTGACGATCATCCAGTGtttt                                            >  1:1916089/1‑34 (MQ=12)
                                                    aCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTgg                          >  1:205362/1‑53 (MQ=255)
                                                    aCATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCAAACTGTTgg                          >  1:4864383/1‑53 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:3982914/1‑46 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:5096688/1‑46 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:827036/1‑46 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCa                                   <  1:2800889/44‑1 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCa                                   <  1:1991530/44‑1 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTg                              >  1:3103883/1‑49 (MQ=255)
                                                    aCATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTg                              >  1:1661717/1‑49 (MQ=255)
                                                     cATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTg       >  1:2768747/1‑71 (MQ=255)
                                                      aTCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCa                                   <  1:3491325/42‑1 (MQ=255)
                                                      aTCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGc      <  1:5090975/71‑1 (MQ=255)
                                                        cgccgcCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:4720874/1‑42 (MQ=255)
                                                        cgccgcCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:3638466/1‑42 (MQ=255)
                                                        cgccgcCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:2764681/1‑42 (MQ=255)
                                                        cgccgcCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:1491933/1‑42 (MQ=255)
                                                        cgccgcCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCata                                 >  1:1536825/1‑42 (MQ=255)
                                                         gccgccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCa                                   >  1:2393787/1‑39 (MQ=255)
                                                         gccgccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCa            >  1:3956571/1‑62 (MQ=255)
                                                          ccgccAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATc  <  1:4935187/71‑1 (MQ=255)
                                                           |                                                                     
GAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTCCCCAGCCTGCCATC  >  minE/1259749‑1259877

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