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 2,595,376 T→C 28.8% I408V (ATC→GTC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,3760TC28.8% 177.2 / 89.0 125I408V (ATC→GTC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base T (43/46);  new base C (19/17);  total (62/63)
Fisher's exact test for biased strand distribution p-value = 6.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

Only 100 of 130 total aligned reads displayed.

ATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCAGAG  >  minE/2595307‑2595445
                                                                     |                                                                     
aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGAt                                                                       <  1:4851837/70‑1 (MQ=255)
aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATa                                                                      <  1:5540100/71‑1 (MQ=255)
  tACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAAt                                                                    >  1:5577178/1‑71 (MQ=255)
   aCAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATc                                                                   >  1:2982070/1‑71 (MQ=255)
   aCAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATc                                                                   >  1:2094823/1‑71 (MQ=255)
    cAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAAtgc                                                                  <  1:3516961/71‑3 (MQ=255)
    cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                                                  <  1:543292/71‑1 (MQ=255)
    cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                                                  >  1:1603561/1‑71 (MQ=255)
       aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                               <  1:4786190/71‑1 (MQ=255)
       aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                               <  1:3202795/71‑1 (MQ=255)
       aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                               <  1:1826622/71‑1 (MQ=255)
        gTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATgccgg                                                               >  1:5242204/1‑68 (MQ=255)
        gTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                               >  1:1153276/1‑70 (MQ=255)
        gTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                               >  1:5256164/1‑70 (MQ=255)
        gTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGt                                                              <  1:969119/71‑1 (MQ=255)
                gagaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAg                                                       >  1:1827920/1‑70 (MQ=255)
                gagaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAg                                                       >  1:825321/1‑70 (MQ=255)
                gagaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGt                                                      <  1:1696360/71‑1 (MQ=255)
                gagaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGt                                                      <  1:163546/71‑1 (MQ=255)
                 agaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTa                                                     <  1:5410098/71‑1 (MQ=255)
                 agaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTa                                                     <  1:1321587/71‑1 (MQ=255)
                       aGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAAt                                                                    >  1:1784388/1‑50 (MQ=255)
                        gcgcCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATccc                                              >  1:5127962/1‑71 (MQ=255)
                        acgcCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATccc                                              >  1:3025161/2‑71 (MQ=255)
                           ccAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAg                                           >  1:4473558/1‑71 (MQ=255)
                             aGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCt                                         <  1:130726/71‑1 (MQ=255)
                              gcgcGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATcccc                                             <  1:4704743/66‑1 (MQ=255)
                              gcgcAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCt                                         >  1:2839713/1‑70 (MQ=255)
                               cgcAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGa                                       <  1:513441/71‑1 (MQ=255)
                               cgcAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGa                                       <  1:29933/71‑1 (MQ=255)
                                 cagccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCt                                                                <  1:2041747/44‑1 (MQ=255)
                                 cagccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGa                                       >  1:5070701/1‑69 (MQ=255)
                                  ggccagaGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGAttg                                    >  1:3870623/2‑69 (MQ=255)
                                     cagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGCTAGTCa                                 <  1:5555/71‑1 (MQ=255)
                                      agcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCa                                 <  1:396040/70‑1 (MQ=255)
                                      agcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCa                                 <  1:1674147/70‑1 (MQ=255)
                                      agcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCa                                 >  1:5646237/1‑70 (MQ=255)
                                       gcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCata                               <  1:4893225/71‑1 (MQ=255)
                                        cGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCatat                              <  1:614030/71‑1 (MQ=255)
                                        cGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCatat                              <  1:1256084/71‑1 (MQ=255)
                                         gTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCatat                              <  1:2985680/70‑1 (MQ=255)
                                          tgacaAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTaa                                                    >  1:60203/3‑47 (MQ=16)
                                          tgacaAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATcccc                                             <  1:4123704/52‑1 (MQ=255)
                                          tgacaAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAttt                            <  1:1203956/69‑2 (MQ=255)
                                          tCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttc                            <  1:1791542/71‑1 (MQ=255)
                                           cacaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTc                                  >  1:5575767/1‑64 (MQ=255)
                                            acaAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAttttt                          <  1:3852905/71‑1 (MQ=255)
                                            acaAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAtttt                           <  1:2152288/70‑3 (MQ=255)
                                            acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGaa                                                        >  1:1390253/1‑41 (MQ=255)
                                            acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGaa                                                        >  1:1231302/1‑41 (MQ=255)
                                            acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGaa                                                        >  1:2766781/1‑41 (MQ=255)
                                            acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttctt                          >  1:4167808/1‑71 (MQ=255)
                                            acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttctt                          >  1:4352398/1‑71 (MQ=255)
                                            acaAACAGCACAGGCAGGGTCATGATAATCCCTGAACGGAAGTAATATcc                                               >  1:5395728/1‑50 (MQ=255)
                                            acaAACAGCAAAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttctt                          >  1:2334813/1‑71 (MQ=255)
                                             caAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAtttttc                         <  1:3068514/71‑1 (MQ=255)
                                             caAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttcttc                         >  1:2882560/1‑71 (MQ=255)
                                              aaaCAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATttttct                        >  1:4119604/1‑71 (MQ=255)
                                              aaaCAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATttttct                        >  1:760969/1‑71 (MQ=255)
                                              aaaCAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATttttct                        >  1:1942030/1‑71 (MQ=255)
                                               aaCAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATcc                                               >  1:4917045/1‑47 (MQ=255)
                                               aaCAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTg                       >  1:1783083/1‑71 (MQ=255)
                                                aCAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGc                      >  1:4643370/1‑71 (MQ=255)
                                                  aGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTggg                     >  1:74608/1‑68 (MQ=255)
                                                  aGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTggg                     >  1:4332141/1‑68 (MQ=255)
                                                     acaGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATtcttct                        >  1:34713/1‑64 (MQ=255)
                                                       aggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGt                                   <  1:2549641/51‑1 (MQ=255)
                                                        ggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTAc              <  1:1130225/71‑1 (MQ=255)
                                                        ggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTAc              <  1:4430395/71‑1 (MQ=255)
                                                         gcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACg             <  1:5252685/71‑1 (MQ=255)
                                                          caggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGt            <  1:1486229/71‑1 (MQ=255)
                                                          caggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGt            <  1:4120927/71‑1 (MQ=255)
                                                           aggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCata                               >  1:2803758/1‑51 (MQ=255)
                                                           aggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCata                               >  1:3604778/1‑51 (MQ=255)
                                                           acagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATg           <  1:5285263/68‑1 (MQ=255)
                                                           acagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATg           <  1:555069/68‑1 (MQ=255)
                                                            gggTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGc          <  1:1524422/71‑1 (MQ=255)
                                                            cagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATg           <  1:2483560/68‑1 (MQ=255)
                                                            cagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGc          <  1:725182/69‑1 (MQ=255)
                                                            cagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGc          <  1:52761/69‑1 (MQ=255)
                                                             tgTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTAc              <  1:2257996/65‑1 (MQ=255)
                                                             ggTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttc                            <  1:3415756/52‑1 (MQ=255)
                                                               tCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGaa                   <  1:5615276/59‑1 (MQ=255)
                                                               tCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAg                 >  1:2554648/1‑61 (MQ=255)
                                                                cATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGc       >  1:3535977/1‑70 (MQ=255)
                                                                 aTGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTc                                  >  1:4134779/1‑42 (MQ=255)
                                                                 aTGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTc                                  >  1:431553/1‑42 (MQ=255)
                                                                 aTGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCa     <  1:5321996/71‑1 (MQ=255)
                                                                 aTGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATg           >  1:833614/1‑65 (MQ=255)
                                                                 aTGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCa     <  1:203005/71‑1 (MQ=255)
                                                                  tGATAATCCCTGTACGGAAGTAATATCCCCAGCTg                                        <  1:3026791/35‑1 (MQ=255)
                                                                  tGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCata                               <  1:4453964/44‑1 (MQ=255)
                                                                    aTAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCa                                 <  1:4261952/40‑1 (MQ=255)
                                                                    aTAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttctt                          >  1:3303398/1‑47 (MQ=255)
                                                                    aTAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttctt                          >  1:2099194/1‑47 (MQ=255)
                                                                    aTAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttctt                          >  1:4746272/1‑47 (MQ=255)
                                                                    aTAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCagag  <  1:5564881/71‑1 (MQ=255)
                                                                     tAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                 >  1:5424356/1‑55 (MQ=255)
                                                                     tAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                 >  1:4243826/1‑55 (MQ=255)
                                                                     tAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                 >  1:470386/1‑55 (MQ=255)
                                                                     |                                                                     
ATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCAGAG  >  minE/2595307‑2595445

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