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 2,040,951 T→A 86.0% *120K (TAA→AAA)  yqiH → predicted periplasmic pilin chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,040,9510TA86.0% 241.5 / 28.3 93*120K (TAA→AAA) yqiHpredicted periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base T (8/5);  new base A (43/37);  total (51/42)
Fisher's exact test for biased strand distribution p-value = 7.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

GAAAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCAAA  >  minE/2040882‑2041018
                                                                     |                                                                   
gAAAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTa                                                                    <  1:1545278/71‑1 (MQ=255)
        tGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGAt                                                             >  1:4140306/1‑70 (MQ=255)
           tCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTa                                                                    <  1:30574/60‑1 (MQ=255)
            cAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa                                                                  >  1:252128/1‑61 (MQ=255)
            cAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa                                                                  >  1:4507597/1‑61 (MQ=255)
             aaCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaa                                                        >  1:949379/1‑70 (MQ=255)
             aaCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaa                                                        <  1:1976451/70‑1 (MQ=255)
             aaCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaa                                                        >  1:4094490/1‑70 (MQ=255)
              aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaa                                                      <  1:4845257/71‑1 (MQ=255)
              aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaa                                                      <  1:4061243/71‑1 (MQ=255)
              aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaa                                                       >  1:1626675/1‑70 (MQ=255)
              aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaa                                                       >  1:469536/1‑70 (MQ=255)
               cTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaaa                                                     >  1:14895/1‑71 (MQ=255)
                  ccTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAAtgt                                                  >  1:2271008/1‑71 (MQ=255)
                   cTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAAtgt                                                  <  1:5538508/70‑1 (MQ=255)
                   cTAAAGACAGAGAAACGCTCTTCTATTATAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAAtgt                                                  <  1:3074206/70‑1 (MQ=255)
                     aaaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCAAAAACAGATAAAAAAAATGTGAt                                               >  1:4656484/1‑71 (MQ=255)
                      aaGACAGTGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATg                                              >  1:3044505/1‑71 (MQ=255)
                      aaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATg                                              >  1:4427728/1‑71 (MQ=255)
                      aaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGAAAAAAAAAATGTGATg                                              >  1:544134/1‑71 (MQ=255)
                       aGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGc                                             <  1:121405/71‑1 (MQ=255)
                         aCAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGc                                             >  1:2665961/1‑69 (MQ=255)
                              gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCaa                                           >  1:2928321/1‑66 (MQ=255)
                              gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCAc                                      <  1:3326745/71‑1 (MQ=255)
                               aaaCGCTCATCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGa                                                >  1:1980783/1‑60 (MQ=255)
                                aaCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    <  1:3300712/71‑1 (MQ=255)
                                 aCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaa                                                      <  1:2899372/52‑1 (MQ=255)
                                  cGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:973466/1‑69 (MQ=255)
                                      cttctATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               >  1:4222836/1‑70 (MQ=255)
                                       ttctATTTTAACGTGCGAGAAATACCGCCCTAAACAg                                                               <  1:1398104/37‑1 (MQ=255)
                                       ttctATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               <  1:2574218/69‑1 (MQ=255)
                                         ctATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACg                           >  1:2757046/1‑71 (MQ=255)
                                         ctATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACg                           >  1:3052610/1‑71 (MQ=255)
                                           aTTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCa                         >  1:3293080/1‑71 (MQ=255)
                                            ttttAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaa                                                      <  1:465384/41‑1 (MQ=255)
                                            ttttAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaa                                                       <  1:1333994/40‑1 (MQ=255)
                                            ttttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAAtgt                                                  <  1:1777105/45‑1 (MQ=255)
                                            ttttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAAtgt                                                  <  1:1793537/45‑1 (MQ=255)
                                            ttttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                                 <  1:4933773/62‑1 (MQ=255)
                                              ttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:1382952/1‑57 (MQ=255)
                                              ttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgca                                >  1:1027463/1‑61 (MQ=255)
                                              ttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCAtt                       <  1:5232331/70‑1 (MQ=255)
                                               tAACGTGCTAGAAATACCGCCCAAAACAGATaaaaaa                                                       <  1:4526558/37‑1 (MQ=38)
                                               tAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaaa                                                     >  1:2047600/1‑39 (MQ=255)
                                               tAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaa                                                       <  1:4228065/37‑1 (MQ=255)
                                               tAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaa                                                       <  1:131361/37‑1 (MQ=255)
                                               tAACGTGCGAGAAATACCGCCCAAAACAGATaaaaa                                                        <  1:2272427/36‑1 (MQ=255)
                                                aaCGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa                     <  1:3705534/70‑1 (MQ=255)
                                                aaCGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa                     <  1:1588540/70‑1 (MQ=255)
                                                 aCGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGaa                    <  1:5141504/70‑1 (MQ=255)
                                                 aCGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               <  1:4779672/59‑1 (MQ=255)
                                                 aCGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               <  1:2196288/59‑1 (MQ=255)
                                                       gagaAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCa                                       <  1:2689914/45‑1 (MQ=255)
                                                       gagaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTc             >  1:2546609/1‑71 (MQ=255)
                                                       gagaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTc             >  1:2236794/1‑71 (MQ=255)
                                                        agaAATACCGCCCAAAACAGATAAAAATAATGTGATGCAAGTCACTAt                                   <  1:2528908/48‑1 (MQ=39)
                                                        agaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTAt                                   <  1:5203648/48‑1 (MQ=255)
                                                        agaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCAtt                       <  1:2496125/60‑1 (MQ=255)
                                                         gaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               <  1:3733287/51‑1 (MQ=255)
                                                         gaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               <  1:592354/51‑1 (MQ=255)
                                                         gaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                               <  1:4014255/51‑1 (MQ=255)
                                                         gaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTg           <  1:1656529/71‑1 (MQ=255)
                                                         gaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTg           >  1:1896953/1‑71 (MQ=255)
                                                         gaAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTg           <  1:3789965/71‑1 (MQ=255)
                                                          aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                                 >  1:5458824/1‑48 (MQ=255)
                                                          aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                                 >  1:2432233/1‑48 (MQ=255)
                                                          aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                                 >  1:621530/1‑48 (MQ=255)
                                                          aaaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                                 >  1:3803767/1‑48 (MQ=255)
                                                          aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTc             >  1:2421758/1‑68 (MQ=255)
                                                          aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg          <  1:1253119/71‑1 (MQ=255)
                                                           aaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggc         >  1:3184319/1‑71 (MQ=255)
                                                           aaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg          <  1:1165512/70‑1 (MQ=255)
                                                            aTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAg                                          >  1:4775813/1‑37 (MQ=255)
                                                            aTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCAGTATGCAGCACGCATTGa                     >  1:830547/1‑58 (MQ=255)
                                                            aTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa                     >  1:3690931/1‑58 (MQ=255)
                                                            aTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa                     >  1:2152186/1‑58 (MQ=255)
                                                            aTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa                     >  1:4818377/1‑58 (MQ=255)
                                                              aCCGCCCAAAACAGATAAAAAAAATGTGATGCAAg                                          >  1:4849516/1‑35 (MQ=255)
                                                              aCCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:5200793/1‑41 (MQ=255)
                                                              aCCGCCAAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:3822707/1‑41 (MQ=38)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:2185637/1‑40 (MQ=255)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:586735/1‑40 (MQ=255)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:210396/1‑40 (MQ=255)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:222910/1‑40 (MQ=255)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:3149543/1‑40 (MQ=255)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggcggc      >  1:2478858/1‑70 (MQ=255)
                                                               ccGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg          >  1:1001429/1‑66 (MQ=255)
                                                                cGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcagca                             >  1:5495889/1‑46 (MQ=255)
                                                                 gCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCaa   <  1:2762356/71‑1 (MQ=255)
                                                                 gCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCaa   <  1:1511934/71‑1 (MQ=255)
                                                                  cccAAAACAGATAAAAAAAATGTGATGCAAGTCAc                                      >  1:4146054/1‑35 (MQ=255)
                                                                  cccAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:120105/1‑37 (MQ=255)
                                                                  cccAAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                    >  1:4309006/1‑37 (MQ=255)
                                                                  cccAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCaaa  <  1:424342/71‑1 (MQ=255)
                                                                  cccAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCaa   >  1:3159723/1‑70 (MQ=255)
                                                                     |                                                                   
GAAAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCCAAA  >  minE/2040882‑2041018

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A