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 837,057 G→T 38.6% V80V (GTG→GTT)  narJ → molybdenum‑cofactor‑assembly chaperone subunit (delta subunit) of nitrate reductase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE837,0570GT38.6% 98.9 / 77.5 88V80V (GTG→GTT) narJmolybdenum‑cofactor‑assembly chaperone subunit (delta subunit) of nitrate reductase 1
Reads supporting (aligned to +/- strand):  ref base G (25/29);  new base T (17/17);  total (42/46)
Fisher's exact test for biased strand distribution p-value = 8.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.97e-01

CCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGAGCAGCACGGCTTG  >  minE/836990‑837126
                                                                   |                                                                     
cccAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCa                                                                     <  1:2142867/70‑1 (MQ=255)
cccAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCa                                                                     <  1:5129755/70‑1 (MQ=255)
 ccAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACg                                                                   <  1:3982208/71‑1 (MQ=255)
 ccAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACg                                                                   >  1:4304606/1‑71 (MQ=255)
  cAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCAc                                                                    >  1:1774486/1‑69 (MQ=255)
  cAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCAc                                                                    >  1:528943/1‑69 (MQ=255)
  cAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACgg                                                                  >  1:4123467/1‑71 (MQ=255)
  cAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACgg                                                                  >  1:5328383/1‑71 (MQ=255)
    ggCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCg                                                                <  1:1142602/71‑1 (MQ=255)
     gcgcAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCg                                                                >  1:1429854/1‑70 (MQ=255)
     gcgcAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCg                                                                >  1:1968832/1‑70 (MQ=255)
        cAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATc                                                            <  1:3038748/71‑1 (MQ=255)
        cAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATc                                                            <  1:1273041/71‑1 (MQ=255)
           tACAGCGAACTGTTCGACCGTGGCCGCTCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcg                                                         >  1:5331585/1‑71 (MQ=255)
            aCAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc                                                        >  1:4351798/1‑71 (MQ=255)
             cAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc                                                        <  1:4655449/70‑1 (MQ=255)
             cAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc                                                        <  1:3180810/70‑1 (MQ=255)
             cAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc                                                        >  1:3275029/1‑70 (MQ=255)
             cAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc                                                        >  1:1954183/1‑70 (MQ=255)
                 gAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc                                                        <  1:3267845/66‑1 (MQ=255)
                       ttCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGa                                                      >  1:3726861/1‑62 (MQ=255)
                       ttCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGa                                                      >  1:1313003/1‑62 (MQ=255)
                          gACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGc                                          <  1:347441/71‑1 (MQ=255)
                          gACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGAACGCGGCCAGGc                                          <  1:5569837/71‑1 (MQ=255)
                           aCCGCGGGCGCACCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGc                                          <  1:248931/70‑1 (MQ=255)
                            ccGCGGGCGCACCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGcaa                                        <  1:4219983/71‑3 (MQ=255)
                            ccGCGGGCGCACCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGcaa                                        <  1:2033718/71‑3 (MQ=255)
                              gTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtg                                      <  1:3691372/71‑1 (MQ=255)
                                 gCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtggt                                    <  1:1477056/70‑1 (MQ=255)
                                  gcgcaCCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtggtgg                                  <  1:4929275/70‑1 (MQ=255)
                                  gcgcaCCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtggtgg                                  <  1:2844976/70‑1 (MQ=255)
                                   cgcgCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCg                                                                >  1:4555090/1‑40 (MQ=255)
                                       ccACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACct                              >  1:5264352/1‑70 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtgttgg                                  <  1:5638980/65‑1 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtggtgg                                  <  1:4664664/65‑1 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtgg                                     >  1:3892172/1‑62 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:2444782/1‑71 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:4174436/1‑71 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:3472542/1‑71 (MQ=255)
                                        cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:4472078/1‑71 (MQ=255)
                                        cACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtggtgg                                  <  1:3683966/65‑1 (MQ=255)
                                         aCGTCCCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGcaa                                        >  1:3736215/1‑56 (MQ=255)
                                          cGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgctg                          >  1:3029830/1‑71 (MQ=255)
                                           gTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGc                                          <  1:5464509/54‑1 (MQ=255)
                                            tcgctgctgctgTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGgc                        <  1:1388791/68‑1 (MQ=255)
                                             cgctgctgctgTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGgcg                       >  1:4414028/3‑71 (MQ=255)
                                              gctgctgctgTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtg                                      >  1:3958707/2‑55 (MQ=255)
                                              gctgctgctgTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGgcg                       <  1:1021282/69‑1 (MQ=255)
                                              gctgctgctgTTCGAACATATTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGgcg                       <  1:3803419/69‑1 (MQ=255)
                                              aCTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGc                                          <  1:900444/51‑1 (MQ=255)
                                              aCTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGgcg                       >  1:4511865/1‑70 (MQ=255)
                                               cTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGgcg                       >  1:955244/1‑69 (MQ=255)
                                                tGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtggtgg                                  <  1:4333687/57‑1 (MQ=255)
                                                tGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtggtgg                                  <  1:352813/57‑1 (MQ=255)
                                                tGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAg                    >  1:2359348/1‑71 (MQ=255)
                                                 gctGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGGCGGAg                    >  1:2021444/3‑70 (MQ=255)
                                                 gTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGc                                          <  1:973012/48‑1 (MQ=255)
                                                 gTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGc                                          <  1:2335640/48‑1 (MQ=255)
                                                  ttGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtg                                      >  1:1548587/1‑51 (MQ=255)
                                                  ctGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            <  1:3437199/60‑1 (MQ=255)
                                                  ctGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGGCGGAGt                   <  1:4773093/69‑1 (MQ=255)
                                                  ctGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGGCGGAGTa                  <  1:1249391/70‑1 (MQ=255)
                                                  ctGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGGCGGAGTa                  >  1:2197833/2‑71 (MQ=255)
                                                   tGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTgg                         >  1:2438912/1‑63 (MQ=255)
                                                     cTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACg                <  1:241880/70‑1 (MQ=255)
                                                     cTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGa               <  1:1022181/71‑1 (MQ=255)
                                                     cTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGcaa                                        <  1:1369561/46‑3 (MQ=16)
                                                     cTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGGCGGAGTATGa               <  1:229261/71‑1 (MQ=255)
                                                     cTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACCTGCTGGCGGAGTATGa               <  1:2408335/71‑1 (MQ=255)
                                                       gTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGag              >  1:386382/1‑70 (MQ=255)
                                                       gTTTGAACATGTGCACGGCGAATCCCGCGAC‑‑CGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGagcag           >  1:2686838/1‑71 (MQ=255)
                                                        tttGAACTTGTGCACGGCGAATCCCGCGACCGCGGCCAGGc                                          <  1:1025207/41‑1 (MQ=255)
                                                        tttGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGc                                          <  1:3737028/41‑1 (MQ=255)
                                                        tttGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctg                             <  1:2986800/54‑1 (MQ=255)
                                                        tttGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGag              <  1:2469044/69‑1 (MQ=255)
                                                         ttGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGa                                        >  1:4370747/1‑42 (MQ=255)
                                                         ttGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGagca            <  1:600224/70‑1 (MQ=255)
                                                          tGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGagcag           <  1:2064394/70‑1 (MQ=255)
                                                          cgAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtggtg                                   >  1:5423722/2‑46 (MQ=16)
                                                           gAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGa               <  1:2838369/65‑1 (MQ=255)
                                                             tcATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgc                            >  1:719290/2‑50 (MQ=255)
                                                             aCATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:4525617/1‑50 (MQ=255)
                                                             aCATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:456750/1‑50 (MQ=255)
                                                             aCATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctg                             >  1:2669587/1‑49 (MQ=255)
                                                             aCATGTTCATGCCGAGTCCAGCGATCGCGGCCAGGCAATGGTGGACctgc                            >  1:5371076/1‑50 (MQ=255)
                                                             aCATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgc                            >  1:848913/1‑50 (MQ=255)
                                                             aCATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgc                            >  1:644956/1‑50 (MQ=255)
                                                               aTGTGCACGGCGAATCCCGCGACC‑CGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGAgcagca         <  1:4636300/66‑1 (MQ=255)
                                                                  tgCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGAGCAGCACGGCTTg  <  1:2243148/71‑1 (MQ=255)
                                                                   |                                                                     
CCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTGGCGCAGTACGAGCAGCACGGCTTG  >  minE/836990‑837126

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