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 1,439,816 G→A 23.3% D162D (GAC→GAT) ‡ ompC ← outer membrane porin protein C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,439,8160GA23.3% 280.0 / 72.1 138D162D (GAC→GAT) ‡ompCouter membrane porin protein C
Reads supporting (aligned to +/- strand):  ref base G (50/54);  new base A (22/10);  total (72/66)
Fisher's exact test for biased strand distribution p-value = 4.51e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 138 total aligned reads displayed.

GCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTG  >  minE/1439747‑1439885
                                                                     |                                                                     
gCCACTAGTAAAGCCTTCACAAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGt                                                                      <  1:2417803/71‑1 (MQ=255)
    cTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:901969/1‑71 (MQ=255)
    cTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:4028265/1‑71 (MQ=255)
    cTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:3794781/1‑71 (MQ=255)
       gTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCa                                                                <  1:2827934/70‑1 (MQ=255)
             ccTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                                                   >  1:2616335/1‑61 (MQ=255)
               ttCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaag                                                        >  1:3829570/1‑70 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                                                   >  1:5603419/1‑57 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                                                   >  1:2544921/1‑57 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                                                   >  1:2246951/1‑57 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCaa                                                                   >  1:4472787/1‑57 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:4820904/1‑71 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:4628469/1‑71 (MQ=255)
                 cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:4258669/1‑71 (MQ=255)
                  aCCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGt                                                    <  1:5050667/71‑1 (MQ=255)
                  aCCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGt                                                    <  1:4362760/71‑1 (MQ=255)
                   ccAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGt                                                    >  1:4219703/1‑70 (MQ=255)
                      gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:1593116/1‑53 (MQ=255)
                      gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaag                                                        <  1:2264004/63‑1 (MQ=255)
                      gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaag                                                        <  1:4076419/63‑1 (MQ=255)
                      gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgt                                                >  1:1500305/1‑71 (MQ=255)
                      gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgt                                                >  1:829005/1‑71 (MQ=255)
                      gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCCTCAACCAGACCgaag                                                        <  1:3613102/63‑1 (MQ=255)
                       aTGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTc                                                                     <  1:3463405/49‑1 (MQ=255)
                        tGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt                                              <  1:594962/71‑1 (MQ=255)
                          ggTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTa                                            <  1:2939076/71‑1 (MQ=255)
                            ttGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCa                                                  <  1:5095300/63‑1 (MQ=255)
                              ttcGTTGTTACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAgt                                                <  1:1222257/61‑1 (MQ=2)
                              ttcGTTGTTACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACga                                         >  1:1921524/3‑69 (MQ=255)
                              gCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg                                         <  1:2365396/70‑1 (MQ=255)
                               tcGTTGTTACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACgat                                        >  1:5514461/2‑68 (MQ=2)
                               ccGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaa                                                         <  1:3448231/53‑1 (MQ=255)
                                cGTTGTTACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACgat                                        >  1:2673864/1‑67 (MQ=9)
                                 gttgttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATaa                                      <  1:913249/70‑2 (MQ=255)
                                 gTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAgg                                     >  1:4051572/1‑71 (MQ=255)
                                 gTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAgg                                     >  1:3481802/1‑71 (MQ=255)
                                  tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCg                                                           <  1:1208302/48‑1 (MQ=255)
                                  tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAgg                                     >  1:3235629/1‑70 (MQ=255)
                                  tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGt                                    >  1:3365252/1‑71 (MQ=255)
                                  tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGt                                    <  1:5418776/71‑1 (MQ=255)
                                  ttattACCCTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGt                                    >  1:5490431/4‑71 (MQ=255)
                                   tattACCCTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGtt                                   >  1:2472725/3‑70 (MQ=255)
                                    tttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCa                                                                >  1:2124127/1‑41 (MQ=255)
                                    tttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcg                                  >  1:5234665/1‑71 (MQ=255)
                                    tttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcg                                  >  1:2293748/1‑71 (MQ=255)
                                    gttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcg                                  >  1:1540319/2‑71 (MQ=255)
                                    gttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcg                                  >  1:2122834/2‑71 (MQ=255)
                                    gttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTc                                   <  1:4359271/69‑1 (MQ=255)
                                    gttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTc                                   <  1:1903393/69‑1 (MQ=255)
                                     ttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcgc                                 <  1:5324948/71‑1 (MQ=9)
                                     ttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaa                                                         <  1:755752/47‑1 (MQ=255)
                                      tACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcgc                                 >  1:1432098/1‑70 (MQ=9)
                                       aCCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcgcg                                <  1:1728528/70‑1 (MQ=255)
                                       aCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcgcg                                >  1:77650/1‑70 (MQ=255)
                                       aCCCTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgcaa                               >  1:4607544/1‑69 (MQ=9)
                                        cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGCAGAAGTCAGTGTTACGGTAGGTCGCGaa                              <  1:4488359/71‑1 (MQ=255)
                                        cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGtt                                             <  1:1886572/56‑1 (MQ=255)
                                        cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcgc                                 <  1:2288497/68‑1 (MQ=255)
                                        cccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgcaa                               <  1:446008/70‑3 (MQ=255)
                                           tgatACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGc                            >  1:4504168/4‑70 (MQ=9)
                                            ggTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTa                                            >  1:2497059/1‑53 (MQ=255)
                                            gatACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAGTCAGTATTACGATAAGTCGCGACGcca                          >  1:3367110/3‑70 (MQ=9)
                                             gTACTGAACAGCAAAGTTCAGGCCTTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         <  1:2621710/71‑1 (MQ=255)
                                             gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGcc                           <  1:1149380/69‑1 (MQ=255)
                                             gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         >  1:3983863/1‑71 (MQ=255)
                                             gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         <  1:798438/71‑1 (MQ=255)
                                              tACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCGGTGTTACGGTAGGTCGCGAAGc                            <  1:5030844/67‑1 (MQ=255)
                                              tACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGtt                        <  1:2037482/71‑1 (MQ=255)
                                               aCTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGaa                              >  1:5538641/1‑64 (MQ=255)
                                                cTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg                                         <  1:4804220/52‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaa                                                         <  1:5518907/35‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc                                                   <  1:1269071/41‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc                                                   <  1:2209405/41‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAg                                                 <  1:1015214/43‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGc                            <  1:5188134/64‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGc                            <  1:4635692/64‑1 (MQ=255)
                                                 tGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGtt                        <  1:1523523/68‑1 (MQ=255)
                                                   aaCAGCAAAGTTCAGGCCGTGAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGaa                              >  1:4705293/1‑60 (MQ=255)
                                                   aaCAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGaa                              >  1:4595357/1‑60 (MQ=255)
                                                   aaCAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGaa                              >  1:1589268/1‑60 (MQ=255)
                                                   aaCAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCAc                   >  1:4472473/1‑71 (MQ=255)
                                                    aCAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgt                                                >  1:316611/1‑41 (MQ=255)
                                                     cAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACgc                 <  1:5579924/71‑1 (MQ=255)
                                                     aaGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAgg                                     >  1:1010531/2‑51 (MQ=255)
                                                     aaGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAgg                                     >  1:3497126/2‑51 (MQ=255)
                                                     aaGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAgg                                     >  1:72759/2‑51 (MQ=255)
                                                     aaGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAgg                                     >  1:3733531/2‑51 (MQ=255)
                                                     aaGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAgg                                     >  1:5216332/2‑51 (MQ=255)
                                                       gCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         >  1:4543191/1‑61 (MQ=255)
                                                           aGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg                                         <  1:1747386/41‑1 (MQ=255)
                                                           aGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg                                         <  1:1058974/41‑1 (MQ=255)
                                                           aGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGtt                                   >  1:4334623/1‑46 (MQ=255)
                                                               cAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATg        >  1:3495420/1‑70 (MQ=255)
                                                               cAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATg        >  1:798367/1‑70 (MQ=255)
                                                                 ggCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAg     <  1:5264623/71‑1 (MQ=255)
                                                                 ggCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAg     <  1:3414457/71‑1 (MQ=255)
                                                                   ccGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGt    >  1:3921721/1‑70 (MQ=255)
                                                                    cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  >  1:625381/1‑71 (MQ=255)
                                                                    cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  <  1:1414085/71‑1 (MQ=255)
                                                                    cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  <  1:5125337/71‑1 (MQ=255)
                                                                     |                                                                     
GCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTG  >  minE/1439747‑1439885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A