BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008736.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,415,379 number of mapped reads = 1,035,254 (73.14%) number of supplementary alignments = 4,014 (0.28%) number of secondary alignments = 0 number of mapped bases = 64,048,295 bp number of sequenced bases = 64,007,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,249 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.159 >>>>>>> ACTG content number of A's = 17,040,692 bp (26.62%) number of C's = 10,962,015 bp (17.13%) number of T's = 19,951,259 bp (31.17%) number of G's = 16,050,223 bp (25.08%) number of N's = 3,002 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 621,561 number of insertions = 5,464 mapped reads with insertion percentage = 0.52% number of deletions = 25,890 mapped reads with deletion percentage = 2.47% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2266X There is a 1.79% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5691034 0.022832577014923465 0.3010752733999064 chr2 243199373 5365911 0.022063835666221065 0.3044377905950642 chr3 198022430 4937766 0.02493538737000652 0.18880384464531544 chr4 191154276 3504793 0.018334891969667474 0.16428488723360024 chr5 180915260 3354089 0.018539558244008825 0.16028777233887284 chr6 171115067 3715967 0.021716188206851474 0.19702700843570262 chr7 159138663 3841668 0.024140381272400157 0.3719984164273472 chr8 146364022 4434910 0.030300547493836975 0.2535540708109854 chr9 141213431 2492991 0.017654064364458363 0.22158891376591383 chr10 135534747 3317397 0.024476358081075695 0.21564126541530323 chr11 135006516 2787015 0.02064355915976678 0.23520725464038536 chr12 133851895 2993611 0.022365099874006266 0.1835149643354892 chr13 115169878 1806136 0.015682364446022945 0.15351051660458953 chr14 107349540 1997822 0.018610438386601376 0.16500318209946743 chr15 102531392 1709162 0.016669645916832964 0.15802430306467072 chr16 90354753 1573690 0.0174167926727662 0.16443357754281304 chr17 81195210 1690842 0.020824405774675623 0.1873750705652085 chr18 78077248 1304557 0.01670854228878559 0.3088354612596337 chr19 59128983 1191245 0.02014654978929707 0.21374172579627543 chr20 63025520 1395965 0.022149202418321974 0.1781275032475369 chr21 48129895 713113 0.014816425425403484 0.14949228710809045 chr22 51304566 676083 0.013177832943757871 0.13406678927873572 chrMT 16571 27677 1.6702069881117616 1.800900736145434 chrX 155270560 3343082 0.021530688109838724 0.18838796822700485 chrY 59373566 181769 0.0030614465703474843 0.07553639797160235