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 1,556,173 A→C 28.4% intergenic (+23/+1240) dsdA → / ← emrY D‑serine ammonia‑lyase/predicted multidrug efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,556,1730AC28.4% 97.5 / 55.3 88intergenic (+23/+1240)dsdA/emrYD‑serine ammonia‑lyase/predicted multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base A (21/42);  new base C (3/22);  total (24/64)
Fisher's exact test for biased strand distribution p-value = 6.21e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.34e-01

Only 100 of 126 total aligned reads displayed.

GGTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGCTATA  >  minE/1556105‑1556240
                                                                    |                                                                   
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:3213687/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:506272/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:1504828/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:2810725/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:2782654/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:2450209/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:2012984/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:723829/69‑1 (MQ=255)
ggTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:2508622/69‑1 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:629783/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:809230/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2434488/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2400361/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:1892407/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:1906781/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:328814/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:640040/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2040806/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2165821/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2146901/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2434854/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:1440481/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2528430/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2680375/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2682113/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:1321423/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:1306374/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2705316/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCaa                                                                    >  1:2863259/1‑69 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     <  1:1494836/68‑1 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCa                                                                     >  1:2339745/1‑68 (MQ=255)
 gTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGATTCAACGCAGCATCGCaa                                                                    >  1:2337644/1‑69 (MQ=255)
      ggAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                <  1:2188308/68‑1 (MQ=255)
      ggAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                <  1:298180/68‑1 (MQ=255)
      ggAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                <  1:422676/68‑1 (MQ=255)
      ggAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                <  1:1091856/68‑1 (MQ=255)
      ggAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                <  1:1357326/68‑1 (MQ=255)
             gagaTGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTgg                                                        >  1:3334624/1‑69 (MQ=255)
             gagaTGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTgg                                                        >  1:1036683/1‑69 (MQ=255)
             gagaTGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTgg                                                        >  1:1812802/1‑69 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:3393155/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:2988535/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:90920/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:2877640/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:2700537/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:840827/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:823529/69‑1 (MQ=255)
                      cAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGAt                                               <  1:1571124/69‑1 (MQ=255)
                             tgtcAAAAGGCCGTTAATAACGTTTCAACGCGGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGcc                                         <  1:2363432/65‑1 (MQ=255)
                             tagCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:2090153/3‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:2040563/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:370663/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:89740/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:3173559/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:2135623/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:2617231/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCt                                                                >  1:1276188/1‑45 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGcc                                         <  1:1610326/68‑1 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGcc                                         <  1:540428/68‑1 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGcc                                         <  1:64355/68‑1 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGcc                                         <  1:2086841/68‑1 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGcc                                         <  1:3420976/68‑1 (MQ=255)
                             tGGCAAAAGGCCGTTAATAACGTTTCAACGAAGCATCGCAATCCt                                                                >  1:2184572/1‑45 (MQ=255)
                                 aaaaGGCGGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2505849/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:3295597/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:1083237/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:3039960/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:393956/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:1678201/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:1184530/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2390416/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2384257/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:787556/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2011753/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2723758/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2799644/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:1188342/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:2022304/67‑1 (MQ=255)
                                 aaaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGGGAGCGATGCTGCCGAt                                      <  1:1401376/67‑1 (MQ=255)
                                  aaaGGCCGTTAATAACGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGAt                                      <  1:277843/66‑1 (MQ=255)
                                       ccGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGa                              <  1:3308971/69‑1 (MQ=255)
                                       ccGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGa                              <  1:543290/69‑1 (MQ=255)
                                              taaCGTTTCAACGCAGCATCGCCATCCTTTCCCTGGGTGAGCGATGCTGCCGATGACGCAGACTTAAGa                       >  1:1424687/1‑69 (MQ=255)
                                                     tCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCgg                >  1:2174566/1‑69 (MQ=255)
                                                     tCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGAGGGCGCAGACTTAAGATCCCCgg                >  1:2819658/1‑69 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:103984/69‑1 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:2203851/69‑1 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:1964721/69‑1 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:1742327/69‑1 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:1604287/69‑1 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:1437227/69‑1 (MQ=255)
                                                         cGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:1190813/69‑1 (MQ=255)
                                                               aTCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATc                     <  1:2174176/54‑1 (MQ=255)
                                                               aTCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGc      <  1:3191610/69‑1 (MQ=255)
                                                               aTCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGc      <  1:3036239/69‑1 (MQ=255)
                                                               aTCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGc      <  1:2334974/69‑1 (MQ=255)
                                                               aTCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGc      <  1:1492439/69‑1 (MQ=255)
                                                                tCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGc      <  1:1122236/68‑1 (MQ=255)
                                                                   cAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCtt            <  1:928511/59‑1 (MQ=255)
                                                                    aaTCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGCtata  <  1:2437751/68‑1 (MQ=255)
                                                                    |                                                                   
GGTGCCGGAAGAAGAGATGAATCAATATCTGGCAAAAGGCCGTTAATAACGTTTCAACGCAGCATCGCAATCCTTTCCCTGGGTGAGCGATGCTGCCGATGGCGCAGACTTAAGATCCCCGGTCTTACCCGCTATA  >  minE/1556105‑1556240

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