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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,541,559 G→A *201* (TAG→TAA)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,541,5590GA100.0% 194.4 / NA 60*201* (TAG→TAA) fimBtyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/32);  total (28/32)

ATACGCGACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAGAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTG  >  NC_000913/4541426‑4541656
                                                                                                                                     |                                                                                                 
aTACGCGACTTATCCAGGATTATCTTGGGCATCGCAATATACGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGTATAGAACCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATa                                                                                              <  1:1009364/139‑1 (MQ=255)
  aCGCGACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAgg                                                                                            <  2:968598/139‑2 (MQ=255)
    gcgANNNATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTg                                                                                          <  2:749055/139‑1 (MQ=255)
      gACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        <  2:166885/139‑1 (MQ=255)
                      tCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        >  2:192205/1‑123 (MQ=255)
                      tCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        <  1:192205/123‑1 (MQ=255)
                      tCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATAc                                                                                    <  2:355823/127‑1 (MQ=255)
                      tCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATAc                                                                                    >  1:355823/1‑127 (MQ=255)
                      tCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGgtgt                                                                        >  2:1411758/1‑139 (MQ=255)
                      tCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGgtgt                                                                        >  2:1355175/1‑139 (MQ=255)
                           ggCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              <  2:545778/128‑1 (MQ=255)
                           ggCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              >  1:545778/1‑128 (MQ=255)
                                cGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTAc                                                              >  1:1422572/1‑139 (MQ=255)
                                  cAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACat                                                            <  1:1355175/139‑1 (MQ=255)
                                          gTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTaaa                                                                    <  1:1074148/123‑1 (MQ=255)
                                          gTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTaaa                                                                    >  2:1074148/1‑123 (MQ=255)
                                            cATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACg                                                  <  1:1411758/139‑1 (MQ=255)
                                               aCTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         >  2:652287/1‑97 (MQ=255)
                                               aCTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         <  1:652287/97‑1 (MQ=255)
                                                 tGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACa                                                             >  2:930095/1‑123 (MQ=255)
                                                 tGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACa                                                             <  1:930095/123‑1 (MQ=255)
                                                   tCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              <  2:750135/104‑1 (MQ=255)
                                                   tCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              >  1:750135/1‑104 (MQ=255)
                                                     tGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        >  1:1459894/1‑92 (MQ=255)
                                                     tGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        <  2:1459894/92‑1 (MQ=255)
                                                        tataCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACatt                                                           >  2:153000/1‑118 (MQ=255)
                                                        tataCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACatt                                                           <  1:153000/118‑1 (MQ=255)
                                                           aCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         >  2:821909/1‑85 (MQ=255)
                                                           aCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         <  1:821909/85‑1 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        <  1:461859/84‑1 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                        >  2:461859/1‑84 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              >  1:1449848/1‑94 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              <  2:1449848/94‑1 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCaaaa                                       >  2:1075458/1‑133 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCaaaa                                       <  1:1075458/133‑1 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGAtt                                 <  2:1422572/139‑1 (MQ=255)
                                                             cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGAtt                                 >  2:935828/1‑139 (MQ=255)
                                                               ccAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTaa                               >  2:1392115/1‑139 (MQ=255)
                                                                           ggCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAAt                   <  1:935828/139‑1 (MQ=255)
                                                                             cGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTg                 >  1:1471332/1‑139 (MQ=255)
                                                                                 tttACGGCATCTGGTATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTg                                                                                          >  1:914729/1‑62 (MQ=255)
                                                                                 tttACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTg                                                                                          <  2:914729/62‑1 (MQ=255)
                                                                                    aCGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTAt          <  1:1392115/139‑1 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGt                                                                                            <  1:355490/51‑1 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGt                                                                                            >  2:355490/1‑51 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         <  2:154193/54‑1 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         >  1:154193/1‑54 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         >  1:989502/1‑54 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                         <  2:989502/54‑1 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCaaaa                                       <  1:1469198/104‑1 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCaaaa                                       >  2:1469198/1‑104 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGt             >  1:831280/1‑130 (MQ=255)
                                                                                          tCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGt             <  2:831280/130‑1 (MQ=255)
                                                                                            ttggATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATTGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAgtg  <  2:1471332/137‑1 (MQ=255)
                                                                                                    agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              <  1:1508784/55‑1 (MQ=255)
                                                                                                    agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                              >  2:1508784/1‑55 (MQ=255)
                                                                                                    agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGAt               <  1:624000/118‑1 (MQ=255)
                                                                                                    agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGAt               >  2:624000/1‑118 (MQ=255)
                                                                                                                              ttttATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAAc                              <  1:1145231/77‑1 (MQ=255)
                                                                                                                              ttttATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAAc                              >  2:1145231/1‑77 (MQ=255)
                                                                                                                                     |                                                                                                 
ATACGCGACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAGAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTG  >  NC_000913/4541426‑4541656

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A