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 2,918,724 G→A 25.4% I324I (ATC→ATT)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,918,7240GA25.4% 192.6 / 64.0 110I324I (ATC→ATT) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base G (44/38);  new base A (21/7);  total (65/45)
Fisher's exact test for biased strand distribution p-value = 7.38e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.42e-01

Only 100 of 112 total aligned reads displayed.

GTTTGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGTG  >  minE/2918656‑2918793
                                                                    |                                                                     
  ttGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAg                                                                   >  1:3224325/1‑71 (MQ=255)
    gTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGt                                                                  <  1:3399092/70‑1 (MQ=255)
       tttCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATg                                                               <  1:4386006/70‑1 (MQ=255)
         tCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTa                                                                 >  1:2017864/1‑66 (MQ=255)
         tCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCa                                                             >  1:5341780/1‑70 (MQ=255)
         tCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCa                                                             >  1:3341005/1‑70 (MQ=255)
           ccGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATAc                                                          <  1:5545724/71‑1 (MQ=255)
               cATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGtt                                                      >  1:4954906/1‑71 (MQ=255)
                aTCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGttt                                                     <  1:2768712/71‑1 (MQ=255)
                aTCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGttt                                                     >  1:2628298/1‑71 (MQ=255)
                aTCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGttt                                                     <  1:3802137/71‑1 (MQ=255)
                 tCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGttt                                                     <  1:4029539/70‑1 (MQ=255)
                  cTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTa                                                                 >  1:2053410/1‑57 (MQ=255)
                   tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAg                                                                   >  1:329472/1‑54 (MQ=255)
                   tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAg                                                                   >  1:350076/1‑54 (MQ=255)
                   tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGtt                                                      >  1:3318140/1‑67 (MQ=255)
                   tttATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTcc                                                  >  1:2134231/1‑71 (MQ=255)
                     tataGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGa                                                                      <  1:1345715/49‑1 (MQ=255)
                     tataGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGa                                                                      <  1:2884489/49‑1 (MQ=255)
                     tataGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGa                                                                      >  1:2306536/1‑49 (MQ=255)
                     tataGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGa                                                                      <  1:2512428/49‑1 (MQ=255)
                     tataGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGa                                                                      <  1:5553535/49‑1 (MQ=255)
                     tataGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGa                                                                      >  1:3878840/1‑49 (MQ=255)
                       taGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTAGATa                                                                    >  1:5103857/1‑49 (MQ=255)
                            aTAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATc                                          >  1:877360/1‑70 (MQ=255)
                              aGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCa                                                             >  1:345850/1‑49 (MQ=255)
                               gCAATTATTTACTGAGCGTCGCGCCCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaaa                                       >  1:492088/1‑70 (MQ=255)
                                   ttattTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTcc                                                  >  1:3790499/1‑55 (MQ=255)
                                    tattTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATAc                                                          >  1:3946427/1‑46 (MQ=255)
                                     attTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATg                                >  1:2060654/1‑71 (MQ=255)
                                      tttACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATg                                <  1:644712/70‑1 (MQ=255)
                                      tttACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATAAAAAACAATg                                <  1:4485733/70‑1 (MQ=255)
                                        tACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCt                              <  1:5530519/70‑1 (MQ=255)
                                           tGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATAc                                                          <  1:808261/39‑1 (MQ=255)
                                           tGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATAc                                                          <  1:339861/39‑1 (MQ=255)
                                           tGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTc                                                   >  1:1120100/1‑46 (MQ=255)
                                           caaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcgcc                          >  1:2189689/3‑70 (MQ=255)
                                            gAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTgg                            <  1:5353396/68‑1 (MQ=255)
                                            aaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGcc                                               >  1:4582003/2‑49 (MQ=16)
                                            aaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGcc                                               >  1:353828/2‑49 (MQ=16)
                                            aaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGcc                                               >  1:66774/2‑49 (MQ=16)
                                            aaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTcg                                         <  1:5402266/54‑2 (MQ=255)
                                            aaGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcgccg                         >  1:4261758/2‑69 (MQ=255)
                                             aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGc                                                >  1:4394633/1‑47 (MQ=16)
                                             aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGc                                                >  1:4102399/1‑47 (MQ=16)
                                             aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGc                                                >  1:5206397/1‑47 (MQ=16)
                                             aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGc                                                >  1:3633256/1‑47 (MQ=16)
                                             aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTcg                                         <  1:1345654/54‑2 (MQ=255)
                                             aGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAacac                                    <  1:1100466/59‑1 (MQ=255)
                                             aGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACaa                                  >  1:170761/1‑61 (MQ=255)
                                             aGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTggcgg                         >  1:4924839/1‑70 (MQ=255)
                                             aGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTggcgg                         >  1:3020288/1‑70 (MQ=255)
                                             aGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTggcgg                         <  1:4542014/70‑1 (MQ=255)
                                              gCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCa                       <  1:4845447/71‑1 (MQ=255)
                                               cGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaaaaa                                     >  1:4725549/1‑56 (MQ=255)
                                               cGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCaaaaa                                     >  1:757299/1‑56 (MQ=255)
                                                 gcgcgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCa                       <  1:4935280/67‑1 (MQ=255)
                                                  cgcgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGAtt                   >  1:5627546/1‑71 (MQ=255)
                                                   gcgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACa                                   >  1:1689430/1‑54 (MQ=255)
                                                   gcgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTc                  >  1:5537665/1‑71 (MQ=255)
                                                    cgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCg                 <  1:3463676/71‑1 (MQ=255)
                                                    cgACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCg                 <  1:1460990/71‑1 (MQ=255)
                                                      atcATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAacac                                    <  1:5057015/48‑1 (MQ=255)
                                                       tcATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCaaac              <  1:2630418/70‑2 (MQ=255)
                                                       tcATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTCGTCGAACACGATGCTCGCCGCCGACTCaaac              <  1:4758191/70‑2 (MQ=255)
                                                       ccATCACCGCTTTGATAGTATGCATACGGTTTTCCg                                                 <  1:3980372/36‑1 (MQ=255)
                                                       ccATCACCGCTTTGATAGTATGCATACGGTTTTCCg                                                 <  1:3987317/36‑1 (MQ=255)
                                                       ccATCACCGCTTTGATAGTATGCATACGGTTTTCCg                                                 <  1:3460234/36‑1 (MQ=255)
                                                       ccATCACCGCTTTGATAGTATGCATACGGTTTTCCg                                                 <  1:639647/36‑1 (MQ=255)
                                                        cATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTc                  >  1:376165/1‑66 (MQ=255)
                                                        cATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGaa               >  1:1033733/1‑69 (MQ=255)
                                                        cATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCaaaca             >  1:3187916/1‑69 (MQ=255)
                                                        cATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCaaaca             >  1:1793959/1‑69 (MQ=255)
                                                         aTCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGAc            <  1:195660/71‑1 (MQ=255)
                                                         aTCACCGCTTTGATAGTATGCATACGGTTTTACGCCTGATCAAAAACAATGCTgg                            >  1:3327857/1‑55 (MQ=255)
                                                         aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCgaac                                      >  1:3876414/1‑44 (MQ=255)
                                                         aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCgaac                                      >  1:3346911/1‑44 (MQ=255)
                                                         aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAacacga                                  >  1:4012771/1‑47 (MQ=255)
                                                         aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCaaa               >  1:1322001/1‑68 (MQ=255)
                                                         aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAacac            >  1:4587746/1‑71 (MQ=255)
                                                         aTCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAacac            >  1:1985400/1‑71 (MQ=255)
                                                            aCCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACa                                   >  1:2851831/1‑45 (MQ=255)
                                                            aCCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCt          <  1:4749531/70‑1 (MQ=255)
                                                            aCCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCt          <  1:2302600/70‑1 (MQ=255)
                                                            aCCGCTTTGATAGTATGCATACGGTTTTCCG‑CTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCtca        >  1:5102262/1‑71 (MQ=255)
                                                             ccGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCtca        <  1:447210/71‑1 (MQ=255)
                                                             ccGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCtcg        >  1:2938459/1‑70 (MQ=255)
                                                             ccGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCtcg        >  1:2910214/1‑70 (MQ=255)
                                                              cGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCtcat       >  1:3119782/1‑71 (MQ=255)
                                                              cGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTcg                                         <  1:295088/37‑2 (MQ=16)
                                                               gCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCt                              <  1:4946635/47‑1 (MQ=255)
                                                                cTTTGATAGTATTCATACGGTTTTCCGCCTGATCAAAAACaa                                  >  1:4833172/1‑42 (MQ=255)
                                                                cTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACaa                                  >  1:306636/1‑42 (MQ=255)
                                                                 tttGATAGTATGCATACGGTTTTCCGCCTGATCAAAAAc                                    <  1:3987717/39‑1 (MQ=255)
                                                                 tttGATAGTATGCATACGGTTTTCCGCCTGATCAAAAAc                                    <  1:674663/39‑1 (MQ=255)
                                                                 tttGATAGTATGCATACGGTTTTCCGCCTGATCAAAAAc                                    <  1:1011809/39‑1 (MQ=255)
                                                                 tttGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAg    >  1:2536734/1‑71 (MQ=255)
                                                                   tGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGt   <  1:1198552/70‑1 (MQ=255)
                                                                   tGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGt   <  1:961524/70‑1 (MQ=255)
                                                                    gATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGTg  <  1:2907587/70‑1 (MQ=255)
                                                                    |                                                                     
GTTTGTATTTCCCGGCATCTTTATAGCGATAGCAATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGGCAGATTCGAAGACCTCATCAGTG  >  minE/2918656‑2918793

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