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
A3 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 4,768,040 C→T 30.7% intergenic (+147/‑35) fpvA → / → tpaK TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,768,0400CT30.7% 70.1 / 37.0 52intergenic (+147/‑35)fpvA/tpaKTonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein
Reads supporting (aligned to +/- strand):  ref base C (16/20);  new base T (6/10);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 7.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

ATCGCCTGACGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTAATTACAATTAATCATCGGCTCGTTTAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGGGTGGTCATGTTCATCGACGGC  >  NC_002947_CJ‑RC/4767893‑4768188
                                                                                                                                                   |                                                                                                                                                    
aTCGCCTGACGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAAc                                                                                                                                                      >  3:188526/1‑148 (MQ=255)
    ccTGACGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTAAGCGGATAATAATTc                                                                                                                                                 <  1:172931/149‑1 (MQ=18)
     cTGACGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAAtta                                                                                                                                                 >  7:45644/1‑147 (MQ=255)
      tGACGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAAttat                                                                                                                                                >  8:172344/1‑146 (MQ=255)
        aCGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAAttatta                                                                                                                                              <  5:18224/148‑1 (MQ=255)
        aCGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAAttatta                                                                                                                                              <  8:45644/148‑1 (MQ=255)
         cGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAg                                                                                                                                            <  3:115430/149‑1 (MQ=255)
           ttGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCtt                                                                                                                                               >  6:50945/1‑144 (MQ=255)
               aCGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTaa                                                                                                                                       <  7:172344/148‑1 (MQ=255)
                  cAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACt                                                                                                                                     >  7:58583/1‑147 (MQ=255)
                    aaaaaCCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTcac                                                                                                                                  <  7:31782/148‑1 (MQ=255)
                         ccGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTCTTAAGATTAACTCACACAg                                                                                                                              >  6:5546/1‑147 (MQ=255)
                            cACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGat                                                                                                                         <  1:345434/149‑1 (MQ=255)
                             aCCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCAGATAACAATTATTAAGATTAACTCACACAGGAGata                                                                                                                        <  3:323993/149‑1 (MQ=14)
                               ccACGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGTCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGatat                                                                                                                       <  6:66577/148‑1 (MQ=11)
                                 aGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCat                                                                                                                    <  3:130230/149‑1 (MQ=255)
                                    tGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCatat                                                                                                                  >  6:118210/1‑148 (MQ=255)
                                                 aTTCACTAGTAGTCTCTATTGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCa                                                                                                     <  2:266526/148‑1 (MQ=11)
                                                  ttCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATc                                                                                                   >  4:46085/1‑149 (MQ=255)
                                                       tagtagTCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATcgcgcg                                                                                              <  4:213404/149‑1 (MQ=255)
                                                         gtagtCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATcgcgcg                                                                                              <  5:50945/147‑1 (MQ=255)
                                                         gtagtCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGt                                                                                             >  4:241689/1‑148 (MQ=255)
                                                           agtCTCTATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTg                                                                                            <  8:248353/147‑1 (MQ=255)
                                                             tctcTATGGAGGTCAGGTAAGATTACTATTGACAATTAATCATAGGCTCGTATAATGTGATCAGACCTGGAATTGAGAGCGGATAACAAATCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGacac                                                                                        >  4:251208/1‑149 (MQ=14)
                                                              ctctATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGacac                                                                                        >  7:194006/1‑148 (MQ=255)
                                                               tatATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTAGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCTCCATCGCGCGTGACACTg                                                                                      >  3:228716/3‑149 (MQ=14)
                                                                ctATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTg                                                                                      >  6:44873/1‑148 (MQ=255)
                                                                ctATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTg                                                                                      >  7:23176/1‑148 (MQ=255)
                                                                 tATGGAGGTCAGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGcc                                                                                    >  3:93443/1‑149 (MQ=255)
                                                                           aGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCAt                                                                           <  1:345062/148‑1 (MQ=255)
                                                                           aGGTATGATTACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCAt                                                                           <  4:333693/148‑1 (MQ=255)
                                                                                   ttACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTcgc                                                                   >  7:273225/1‑148 (MQ=255)
                                                                                   ttACTATTGACAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTcgc                                                                   >  6:110423/1‑148 (MQ=255)
                                                                                            aCAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTg                                                           <  5:112740/147‑1 (MQ=255)
                                                                                             cAATTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAg                                                         >  8:226440/1‑148 (MQ=255)
                                                                                              aaTTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGAtt                                                                      <  4:237737/134‑1 (MQ=255)
                                                                                              aaTTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGAtt                                                                      >  3:237737/1‑134 (MQ=255)
                                                                                              aaTTAATCATCGGCTCGTATAATGTGATCAGACCTGAAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTc                                                       <  3:56667/149‑1 (MQ=255)
                                                                                               aTTAATCATCGGCTCGTATAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTc                                                       <  6:185256/148‑1 (MQ=255)
                                                                                                              gtatAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATc                                         <  3:370457/144‑1 (MQ=255)
                                                                                                               tatAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGt                                       <  5:110423/146‑1 (MQ=255)
                                                                                                                 tAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTg                                      <  5:118210/147‑1 (MQ=255)
                                                                                                                    tgtgATCAGACCTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCg                                  >  7:279745/1‑148 (MQ=255)
                                                                                                                      tgATCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGcc                                <  5:347207/148‑1 (MQ=255)
                                                                                                                         tCAGACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCtgt                            <  4:93443/149‑1 (MQ=255)
                                                                                                                            gACCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCtgtgt                          >  5:325088/1‑148 (MQ=255)
                                                                                                                             aCCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATcgcgcg                                                                                              >  7:41917/1‑79 (MQ=255)
                                                                                                                             aCCTGGAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATcgcgcg                                                                                              <  8:41917/79‑1 (MQ=255)
                                                                                                                              acTGGAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTggg                       <  2:377477/148‑1 (MQ=255)
                                                                                                                                  gAATTGTGAGCGGATAATAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGggtg                    <  1:8090/148‑1 (MQ=255)
                                                                                                                                  gAATTGTGAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGggt                     <  5:217466/147‑1 (MQ=255)
                                                                                                                                       gtgAGCGGATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGGGTGGTCa                <  6:196013/147‑1 (MQ=255)
                                                                                                                                              gATAACAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGGGTGGTCATGTTCATc        >  1:39443/1‑148 (MQ=255)
                                                                                                                                                   cAATTATTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGGGTGGTCATGTTCATCGACGGc  >  2:216364/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
ATCGCCTGACGTTGAACGCAAAAAACCGCACCCAGGTGCGGTTTTTTGAATTCACTAGTAGTCTCTATGGAGGTCAGGTATGATTACTAATTACAATTAATCATCGGCTCGTTTAATGTGATCAGACCTGGAATTGTGAGCGGATAACAATTCTTAAGATTAACTCACACAGGAGATATCATATGTCCTTAGCACCATCGCGCGTGACACTGCCGGATTTCATCGATTCGCGGCCAGTGAGTCGATACCAGTACATCGTGATCGCCCTGTGTGGGGTGGTCATGTTCATCGACGGC  >  NC_002947_CJ‑RC/4767893‑4768188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A