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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,099,098 A→G 39.8% G299G (GGT→GGC)  garP ← predicted (D)‑galactarate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,099,0980AG39.8% 42.6 / 68.8 98G299G (GGT→GGC) garPpredicted (D)‑galactarate transporter
Reads supporting (aligned to +/- strand):  ref base A (28/31);  new base G (20/19);  total (48/50)
Fisher's exact test for biased strand distribution p-value = 8.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-03

GGGTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTT  >  minE/2099031‑2099155
                                                                   |                                                         
gggTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCTCAAAAc                                                          <  1:1083977/69‑1 (MQ=255)
gggTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAAc                                                          <  1:3141083/69‑1 (MQ=255)
gggTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAAc                                                          <  1:2741203/69‑1 (MQ=255)
gggTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAAc                                                          <  1:1437061/69‑1 (MQ=255)
gggTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAAc                                                          <  1:880754/69‑1 (MQ=255)
  gTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACca                                                        <  1:412996/69‑1 (MQ=255)
  gTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACca                                                        <  1:325174/69‑1 (MQ=255)
  gTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACca                                                        <  1:324762/69‑1 (MQ=255)
  gTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACca                                                        <  1:2559784/69‑1 (MQ=255)
   tCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACca                                                        <  1:65342/68‑1 (MQ=255)
   tCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCAGCAAAACca                                                        <  1:588255/68‑1 (MQ=255)
     aGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACcacac                                                     >  1:2858740/1‑69 (MQ=255)
     aGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACcacac                                                     >  1:2351201/1‑69 (MQ=255)
         aTAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTg                                                 <  1:2071634/69‑1 (MQ=255)
         aTAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTg                                                 <  1:1099872/69‑1 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2383151/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:181454/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2229980/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2354515/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2378417/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2602527/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2637285/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2878493/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:2970891/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:415542/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:169461/1‑69 (MQ=255)
          tAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGc                                                >  1:1704116/1‑69 (MQ=255)
          caaaCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGc                                                <  1:3190342/68‑1 (MQ=255)
          caaaCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGc                                                <  1:402172/68‑1 (MQ=255)
          caaaCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGc                                                <  1:2018005/68‑1 (MQ=255)
          caaaCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGc                                                <  1:2028908/68‑1 (MQ=255)
          caaaCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGc                                                <  1:758738/68‑1 (MQ=255)
             aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCt                                               >  1:2729425/1‑67 (MQ=255)
             aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTgg                                             >  1:1244358/1‑69 (MQ=255)
             aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTgg                                             >  1:1706415/1‑69 (MQ=255)
             aCCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTgg                                             >  1:779619/1‑69 (MQ=255)
                    ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:1868613/69‑1 (MQ=255)
                    ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:2874470/69‑1 (MQ=255)
                    ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:1561527/69‑1 (MQ=255)
                    ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:475829/69‑1 (MQ=255)
                    ttGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:58726/69‑1 (MQ=255)
                     tGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:1773131/68‑1 (MQ=255)
                     tGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAg                                      <  1:768935/68‑1 (MQ=255)
                     tGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTg                                                 <  1:1982966/57‑1 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCg                                   >  1:2082090/1‑67 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:1352525/69‑1 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:2990655/69‑1 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:194552/69‑1 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:1243216/69‑1 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:2167340/69‑1 (MQ=255)
                         cAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:772332/69‑1 (MQ=255)
                           gATAATCCGAGAAGACACCTCCCAGCACTCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGAc                                 <  1:1589243/67‑1 (MQ=255)
                               aTCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGAcc                           <  1:187159/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:220707/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:1215223/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:2260991/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:1973742/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:1289413/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:2037788/69‑1 (MQ=255)
                                     gaagaCACCTCCCAGCACGCCGCCCGCAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACttt                     <  1:214328/69‑1 (MQ=255)
                                        gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg                  >  1:2649787/1‑69 (MQ=255)
                                        gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg                  >  1:1580357/1‑69 (MQ=255)
                                        gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg                  >  1:2165214/1‑69 (MQ=255)
                                        gaCACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAg                  >  1:128757/1‑69 (MQ=255)
                                          cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGAcc                           >  1:303915/1‑58 (MQ=255)
                                          cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGag                >  1:2906446/1‑68 (MQ=255)
                                          cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGaa                >  1:2770317/1‑69 (MQ=255)
                                          cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGaa                >  1:798740/1‑69 (MQ=255)
                                          cacCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGaa                >  1:246621/1‑69 (MQ=255)
                                              tCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa            <  1:2173098/69‑1 (MQ=255)
                                              tCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa            <  1:1488947/69‑1 (MQ=255)
                                              tCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa            <  1:684888/69‑1 (MQ=255)
                                               cccAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa            <  1:1386835/68‑1 (MQ=255)
                                                ccAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGa            <  1:227554/67‑1 (MQ=255)
                                                        ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt  <  1:390948/69‑1 (MQ=255)
                                                        ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt  <  1:3328746/69‑1 (MQ=255)
                                                        ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt  <  1:1282920/69‑1 (MQ=255)
                                                        ccgcccgcAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCtttt  <  1:971/69‑1 (MQ=255)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2569876/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:180052/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:1969256/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:1783844/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2181460/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:1714281/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:1706240/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:1701748/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:672729/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:312105/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2641202/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2649857/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2749502/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2836220/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2851394/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:286368/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:2902879/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACtt                      >  1:381416/1‑42 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAGGCGACCAGACCCACt                       >  1:2491174/1‑41 (MQ=38)
                                                               cAAAGCCACACAGTGCCGGAATCGAG‑‑GACCAGACCCACtt                      >  1:1411486/1‑40 (MQ=255)
                                                                   |                                                         
GGGTCAGGGATAAACCGCGTTTGATCAGATAATCCGAGAAGACACCTCCCAGCACGCCGCCCGCAAAACCACACAGTGCTGGAATCGAGGCGACCAGACCCACTTTCAGAATCGACATGCCTTTT  >  minE/2099031‑2099155

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