BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514738.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 225,727,008 number of mapped reads = 217,212,695 (96.23%) number of supplementary alignments = 7,921,276 (3.51%) number of secondary alignments = 0 number of mapped bases = 20,449,034,437 bp number of sequenced bases = 20,434,249,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,597,314 duplication rate = 42.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2028 >>>>>>> ACTG content number of A's = 5,311,363,168 bp (25.99%) number of C's = 4,803,031,064 bp (23.5%) number of T's = 5,343,138,623 bp (26.15%) number of G's = 4,827,354,515 bp (23.62%) number of N's = 149,361,878 bp (0.73%) GC percentage = 47.13% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 219,789,283 number of insertions = 8,659,122 mapped reads with insertion percentage = 3.82% number of deletions = 6,280,565 mapped reads with deletion percentage = 2.77% homopolymer indels = 39.29% >>>>>>> Coverage mean coverageData = 6.6056X std coverageData = 206.0853X There is a 18.81% of reference with a coverageData >= 1X There is a 12.81% of reference with a coverageData >= 2X There is a 9.77% of reference with a coverageData >= 3X There is a 8.02% of reference with a coverageData >= 4X There is a 6.85% of reference with a coverageData >= 5X There is a 6.02% of reference with a coverageData >= 6X There is a 5.39% of reference with a coverageData >= 7X There is a 4.9% of reference with a coverageData >= 8X There is a 4.5% of reference with a coverageData >= 9X There is a 4.18% of reference with a coverageData >= 10X There is a 3.91% of reference with a coverageData >= 11X There is a 3.67% of reference with a coverageData >= 12X There is a 3.47% of reference with a coverageData >= 13X There is a 3.3% of reference with a coverageData >= 14X There is a 3.15% of reference with a coverageData >= 15X There is a 3.01% of reference with a coverageData >= 16X There is a 2.89% of reference with a coverageData >= 17X There is a 2.78% of reference with a coverageData >= 18X There is a 2.68% of reference with a coverageData >= 19X There is a 2.59% of reference with a coverageData >= 20X There is a 2.51% of reference with a coverageData >= 21X There is a 2.43% of reference with a coverageData >= 22X There is a 2.36% of reference with a coverageData >= 23X There is a 2.3% of reference with a coverageData >= 24X There is a 2.24% of reference with a coverageData >= 25X There is a 2.18% of reference with a coverageData >= 26X There is a 2.13% of reference with a coverageData >= 27X There is a 2.08% of reference with a coverageData >= 28X There is a 2.03% of reference with a coverageData >= 29X There is a 1.99% of reference with a coverageData >= 30X There is a 1.95% of reference with a coverageData >= 31X There is a 1.91% of reference with a coverageData >= 32X There is a 1.87% of reference with a coverageData >= 33X There is a 1.84% of reference with a coverageData >= 34X There is a 1.8% of reference with a coverageData >= 35X There is a 1.77% of reference with a coverageData >= 36X There is a 1.74% of reference with a coverageData >= 37X There is a 1.71% of reference with a coverageData >= 38X There is a 1.69% of reference with a coverageData >= 39X There is a 1.66% of reference with a coverageData >= 40X There is a 1.63% of reference with a coverageData >= 41X There is a 1.61% of reference with a coverageData >= 42X There is a 1.59% of reference with a coverageData >= 43X There is a 1.56% of reference with a coverageData >= 44X There is a 1.54% of reference with a coverageData >= 45X There is a 1.52% of reference with a coverageData >= 46X There is a 1.5% of reference with a coverageData >= 47X There is a 1.48% of reference with a coverageData >= 48X There is a 1.46% of reference with a coverageData >= 49X There is a 1.44% of reference with a coverageData >= 50X There is a 1.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1191098543 4.778718457034456 145.95741004556362 chr2 243199373 2951618841 12.136621918840227 297.398973509351 chr3 198022430 1908700622 9.63881021963017 201.37222448597373 chr4 191154276 439544383 2.2994221850417826 47.242208712974985 chr5 180915260 1652547430 9.134372799729553 183.13006704142032 chr6 171115067 426847155 2.4945036254463786 69.28364209275287 chr7 159138663 741189382 4.6575066550609385 118.64849802214098 chr8 146364022 356201175 2.4336662120421915 34.55342206117968 chr9 141213431 222835090 1.5780020952822824 67.24241411798145 chr10 135534747 1100343645 8.118535426195912 145.5152636796696 chr11 135006516 784688572 5.812227403898046 134.98963110101616 chr12 133851895 369645683 2.7616021648404754 41.882280929467086 chr13 115169878 155479072 1.3499977138119397 28.16770304540394 chr14 107349540 1346335005 12.54160013168198 141.5864437104848 chr15 102531392 714680353 6.970356483602602 66.70132830202618 chr16 90354753 297346083 3.290873729686362 114.49697051283377 chr17 81195210 2180369474 26.85342490031124 300.83668265096446 chr18 78077248 241343348 3.091084204197361 105.67690407256227 chr19 59128983 891890282 15.083808933429482 100.15740691794781 chr20 63025520 451126387 7.1578368095971285 124.06637462500896 chr21 48129895 196317562 4.078911080109358 69.07728330880201 chr22 51304566 660363044 12.871428324722599 437.3188656036704 chrMT 16571 33506679 2022.0070605274275 732.1045956460214 chrX 155270560 547333637 3.52503164154235 423.3060697606502 chrY 59373566 587682990 9.89805783267254 698.9815833435234