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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,546,724 T→C 41.4% S2S (AGT→AGC)  fimE → 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
*W3110S.gb4,546,7240TC41.4% 55.2 / 115.1 96S2S (AGT→AGC) fimEtyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand):  ref base T (33/23);  new base C (21/17);  total (55/41)
Fisher's exact test for biased strand distribution p-value = 8.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAAC  >  W3110S.gb/4546656‑4546789
                                                                    |                                                                 
tGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTa                                                                  <  1:714085/70‑1 (MQ=255)
       ttGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCaaa                                                                <  1:1269229/65‑1 (MQ=255)
          aGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTAt                                                       <  1:2217654/71‑1 (MQ=255)
             tttGCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTa                                                                  <  1:1258992/57‑1 (MQ=255)
                     aGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTAc                                                  >  1:1888798/1‑65 (MQ=255)
                      ggTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTa                                             >  1:3308914/1‑69 (MQ=255)
                      ggTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTa                                             >  1:1235578/1‑69 (MQ=255)
                      ggTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTa                                             >  1:1655218/1‑69 (MQ=255)
                      ggTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTa                                             >  1:1960395/1‑69 (MQ=255)
                        tATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTa                                             <  1:3011053/67‑1 (MQ=255)
                        tATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaag                                          <  1:1576535/70‑1 (MQ=255)
                         attcattcAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaaga                                         <  1:2816590/70‑1 (MQ=255)
                          ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTaaa                                           >  1:4016884/1‑67 (MQ=255)
                          ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTaaa                                           >  1:2351116/1‑67 (MQ=255)
                          ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGACGTTATCTTACCGGTaaa                                           >  1:2794978/1‑67 (MQ=255)
                            cattcaAATATATCTTAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGtt                                     >  1:3359115/1‑71 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCg                                                >  1:2896452/1‑60 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCg                                                >  1:2973433/1‑60 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt                                     >  1:2953468/1‑71 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt                                     >  1:3790469/1‑71 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGGAAACGTCGTTATCTTACCGGTAAAGAAGtt                                     >  1:3983375/1‑71 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAAcgt                                                             >  1:1865862/1‑47 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTa                                                        >  1:714224/1‑52 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTa                                                        >  1:3925068/1‑52 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTa                                                        >  1:2977801/1‑52 (MQ=255)
                            cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGtt                                     >  1:1914992/1‑71 (MQ=255)
                             attcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGt                                      <  1:36141/69‑1 (MQ=255)
                                caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg                                 >  1:3706858/1‑71 (MQ=255)
                                caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg                                 >  1:138844/1‑71 (MQ=255)
                                caAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg                                 >  1:2343900/1‑71 (MQ=255)
                                  aaTATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGcc                               <  1:599904/71‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGTAAAcgtc                                                            <  1:3350691/40‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:2724138/71‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:3055633/71‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGCaa                                                                 >  1:85869/1‑35 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:1314389/71‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:3977127/71‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:487131/71‑1 (MQ=255)
                                    tatatCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:789897/71‑1 (MQ=255)
                                     atatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTc                                    >  1:1743727/1‑63 (MQ=255)
                                        tctcAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTa                                             <  1:3566087/51‑1 (MQ=255)
                                        tctcAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTa                                             <  1:3055070/51‑1 (MQ=255)
                                        tctcAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:3792907/67‑1 (MQ=255)
                                          tcAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatgatg                         >  1:125694/1‑69 (MQ=255)
                                           cAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAg                      >  1:3915696/1‑71 (MQ=255)
                                            aGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCa                       <  1:1468939/69‑1 (MQ=255)
                                              ttAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:35255/61‑1 (MQ=255)
                                              ttAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:1319694/61‑1 (MQ=255)
                                                aGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga                           >  1:1836442/1‑61 (MQ=255)
                                                aGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga                           >  1:3096520/1‑61 (MQ=255)
                                                aGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga                           >  1:2628652/1‑61 (MQ=255)
                                                  gAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:2793453/57‑1 (MQ=255)
                                                  gAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:3353051/57‑1 (MQ=255)
                                                  gAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:2081393/57‑1 (MQ=255)
                                                    gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt             <  1:1195131/71‑1 (MQ=255)
                                                    gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt             <  1:2610392/71‑1 (MQ=255)
                                                     tactacTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGc                                <  1:4079993/51‑1 (MQ=255)
                                                     tactacTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:3330043/54‑1 (MQ=255)
                                                     tactacTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:822051/54‑1 (MQ=255)
                                                     tactacTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat                             <  1:2713187/54‑1 (MQ=255)
                                                     tactacTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGtt            <  1:410391/71‑1 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGtt                >  1:3449755/1‑65 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGtt                >  1:2480630/1‑65 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt             <  1:3629815/68‑1 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          >  1:1897381/1‑71 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          <  1:556975/71‑1 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          >  1:4054604/1‑71 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          >  1:3995292/1‑71 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          >  1:3642082/1‑71 (MQ=255)
                                                       ctactaTTGTGAGTAAACGTCGTTATCTTAACGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          >  1:2930030/1‑71 (MQ=255)
                                                       ctactaTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc          >  1:1490804/1‑71 (MQ=255)
                                                        tactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatgatg                         <  1:2275778/55‑1 (MQ=255)
                                                          ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag                                       >  1:40531/1‑39 (MQ=255)
                                                          ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt             >  1:1911689/1‑65 (MQ=255)
                                                          ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt             >  1:566505/1‑65 (MQ=255)
                                                          ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt             >  1:876253/1‑65 (MQ=255)
                                                          ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACggg       >  1:788391/1‑71 (MQ=255)
                                                          ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACgg        >  1:953857/1‑70 (MQ=255)
                                                          ctaTTGTGAGCAAACGTCGTTATCTTACCGGTAaagaa                                        >  1:3974962/1‑38 (MQ=255)
                                                          ctaTTGTGAGCAAACGTCGTTATCTTACCGGTAaagaa                                        >  1:676955/1‑38 (MQ=255)
                                                          ctaTTGTGAGCAAACGTCGTTATCTTACCGGTAaagaa                                        >  1:1891597/1‑38 (MQ=255)
                                                          ctaTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGt                 >  1:2094057/1‑61 (MQ=255)
                                                          ctaTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACggg       >  1:3759022/1‑71 (MQ=255)
                                                          ctaTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACggg       >  1:1658789/1‑71 (MQ=255)
                                                           taTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCa                       <  1:201424/54‑1 (MQ=255)
                                                             ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga                           >  1:1141853/1‑48 (MQ=255)
                                                             ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga                           >  1:1546399/1‑48 (MQ=255)
                                                             ttGTGAGGAAACGTCGTTATCTTACCGGTAAAGAAGt                                      <  1:1970489/37‑1 (MQ=255)
                                                             ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGtt                                     <  1:2265399/38‑1 (MQ=255)
                                                             ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGt                                      <  1:3275963/37‑1 (MQ=255)
                                                             ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGt                                      <  1:815460/37‑1 (MQ=255)
                                                              tgtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGt                                      <  1:2677220/36‑1 (MQ=255)
                                                               gtgAGTAAACGTCGTTATCTTACCGGTAAAGAAGt                                      >  1:496535/1‑35 (MQ=255)
                                                               gtgAGTAAACGTCGTTATCTTACCGGTAAAGAAGt                                      >  1:3363858/1‑35 (MQ=255)
                                                               gtgAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAAc  >  1:2100398/1‑71 (MQ=255)
                                                                  aGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCaa   >  1:1653673/1‑67 (MQ=255)
                                                                    tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTa           <  1:1837321/57‑1 (MQ=255)
                                                                    tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTa           <  1:3913093/57‑1 (MQ=255)
                                                                    |                                                                 
TGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAAC  >  W3110S.gb/4546656‑4546789

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