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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 430,231 G→A 45.8% D280N (GAC→AAC)  glnS → glutamyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE430,2310GA45.8% 35.0 / 149.8 107D280N (GAC→AAC) glnSglutamyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base G (29/29);  new base A (22/27);  total (51/56)
Fisher's exact test for biased strand distribution p-value = 6.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

Only 100 of 107 total aligned reads displayed.

TGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTA  >  minE/430164‑430298
                                                                   |                                                                   
tGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGAc                                                                   >  1:1554893/1‑70 (MQ=255)
tGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACa                                                                  <  1:2471886/71‑1 (MQ=255)
  aGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                >  1:382110/1‑71 (MQ=255)
  aGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                >  1:2801079/1‑71 (MQ=255)
    ttCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCa                                                              <  1:461198/71‑1 (MQ=255)
    ttCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCa                                                              <  1:3943773/71‑1 (MQ=255)
    ttCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCa                                                              <  1:2541286/71‑1 (MQ=255)
         gcgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAATCACg                                                            <  1:2095446/68‑1 (MQ=255)
         gcgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTg                                                         <  1:1984668/71‑1 (MQ=255)
            ccTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAg                                                      <  1:2814558/71‑1 (MQ=255)
             cTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAgg                                                     <  1:3721304/71‑1 (MQ=255)
                 aTCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGCCAAGCACGTTGAAGGCTgg                                                 >  1:3448885/1‑71 (MQ=255)
                 aTCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                 <  1:4090434/71‑1 (MQ=255)
                 aTCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                 <  1:2911207/71‑1 (MQ=255)
                 aTCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                 <  1:3834692/71‑1 (MQ=255)
                      gAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATg                                             <  1:3359541/70‑1 (MQ=255)
                      gAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGAt                                              <  1:1368052/69‑1 (MQ=255)
                      gAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGAt                                              <  1:326979/69‑1 (MQ=255)
                       aaTACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGa                                                        <  1:4034871/58‑1 (MQ=255)
                       aaTACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGa                                                        <  1:1699348/58‑1 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAg                                                      >  1:1602315/1‑58 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAg                                                      >  1:3129094/1‑58 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAg                                                      >  1:3189343/1‑58 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAccc                                         >  1:1856206/1‑71 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAcc                                          >  1:2507545/1‑70 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAc                                           <  1:3289472/69‑1 (MQ=255)
                         tACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAc                                           <  1:253658/69‑1 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgc                                       >  1:1217874/1‑71 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:3725854/1‑63 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:2677908/1‑63 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:3985478/1‑63 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:345250/1‑63 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:1035309/1‑63 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:883515/1‑63 (MQ=255)
                           cacCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGa                                               >  1:852897/1‑63 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:1228657/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:3642274/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:1863378/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:564859/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:4084213/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:285924/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:3980446/71‑1 (MQ=255)
                            acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:443745/71‑1 (MQ=255)
                              cGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:1494778/69‑1 (MQ=255)
                                  aTGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGAGAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                <  1:3366428/71‑1 (MQ=255)
                                  aTGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                <  1:1858723/71‑1 (MQ=255)
                                   tGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                >  1:3959451/1‑70 (MQ=255)
                                   tGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                <  1:1125482/70‑1 (MQ=255)
                                   tGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                >  1:637314/1‑70 (MQ=255)
                                   tGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                >  1:4105940/1‑70 (MQ=255)
                                   tGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                >  1:1297003/1‑70 (MQ=255)
                                    gTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCa                                                              >  1:575823/1‑39 (MQ=255)
                                    gTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCa                                                              >  1:2946928/1‑39 (MQ=255)
                                    gTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCa                                                              >  1:3296171/1‑39 (MQ=255)
                                     tCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGAc                             <  1:2323919/71‑1 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:1631091/60‑1 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:3546297/60‑1 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGaa                                                       >  1:2186687/1‑43 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGaa                                                       >  1:1923945/1‑43 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGaa                                                       >  1:2181847/1‑43 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGaa                                                       >  1:3341839/1‑43 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCa                           >  1:75510/1‑71 (MQ=255)
                                       cAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCa                           >  1:396430/1‑71 (MQ=255)
                                        aaGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATg                                             <  1:2431729/52‑1 (MQ=255)
                                        aaGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:4017006/59‑1 (MQ=255)
                                        aaGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:1090405/59‑1 (MQ=255)
                                          gCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTa                                    >  1:3533034/1‑59 (MQ=255)
                                          gCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTa                                    >  1:1874454/1‑59 (MQ=255)
                                           cGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTc                       <  1:2423025/71‑1 (MQ=255)
                                           cGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTc                       <  1:2417799/71‑1 (MQ=255)
                                           cGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTc                       <  1:3106864/71‑1 (MQ=255)
                                             tAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCg                     <  1:1454431/71‑1 (MQ=255)
                                             tAAGTTGAACCTGCTGGTGACCAACAAGCACGTTg                                                         <  1:310142/35‑1 (MQ=255)
                                             tAAGTTGAACCTGCTGGTGACCAACAAGCACGTTg                                                         <  1:2669913/35‑1 (MQ=255)
                                             tAAGTTGAACCTGCTGGTGACCAACAAGCACGTTg                                                         <  1:3076118/35‑1 (MQ=255)
                                              aaGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:3829119/53‑1 (MQ=255)
                                              aaGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                      <  1:2379856/53‑1 (MQ=255)
                                               aGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCgg                    >  1:2165699/1‑70 (MQ=255)
                                                   gAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAccc                                         >  1:3006690/1‑45 (MQ=255)
                                                   gAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAccc                                         >  1:3001865/1‑45 (MQ=255)
                                                   gAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGAccc                                         >  1:3312809/1‑45 (MQ=255)
                                                        tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGa                                            >  1:3280944/1‑37 (MQ=255)
                                                        tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGa                                            >  1:1920742/1‑37 (MQ=255)
                                                        tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGa                                            >  1:3366136/1‑37 (MQ=255)
                                                        tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtc            <  1:1648640/69‑1 (MQ=255)
                                                        tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtc            <  1:1125148/69‑1 (MQ=255)
                                                        tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtc            <  1:3436702/69‑1 (MQ=255)
                                                        tgctgGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGcc                                >  1:2694603/1‑49 (MQ=255)
                                                         gctgGTGACCGACAAGCACGTTGAAGGCTGGGATGAcc                                          >  1:3968388/1‑38 (MQ=255)
                                                         gctgGTGACCGACAAGCACGTTGAAGGCTGGGATGAcc                                          >  1:3866741/1‑38 (MQ=255)
                                                         gctgGTGACCGACAAGCACGTTGAAGGCTGGGATGAcc                                          >  1:3278741/1‑38 (MQ=255)
                                                         gctgGTGACCGACAAGCACGTTGAAGGCTGGGATGAcc                                          >  1:1472732/1‑38 (MQ=255)
                                                         gctgGTGACCGACAAGCACGTTGAAGGCTGGGATGAcc                                          >  1:3683139/1‑38 (MQ=255)
                                                         gctgGTGACCGACAAGCACGTTGAAGGCTCGGATGAcc                                          >  1:2698844/1‑38 (MQ=255)
                                                          ctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtcgt          >  1:3339572/1‑69 (MQ=255)
                                                          ctgGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtcgtcg        <  1:3795564/71‑1 (MQ=255)
                                                           tgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTc                  <  1:2434396/60‑1 (MQ=255)
                                                              tGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtc            <  1:2518470/63‑1 (MQ=255)
                                                                aCCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTa  <  1:2305967/71‑1 (MQ=255)
                                                                 ccGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTa  >  1:453699/1‑70 (MQ=255)
                                                                   |                                                                   
TGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTA  >  minE/430164‑430298

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