BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008707.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 = 1,172,604 number of mapped reads = 932,581 (79.53%) number of supplementary alignments = 3,386 (0.29%) number of secondary alignments = 0 number of mapped bases = 59,436,053 bp number of sequenced bases = 59,404,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,161 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1051 >>>>>>> ACTG content number of A's = 16,731,879 bp (28.17%) number of C's = 9,981,049 bp (16.8%) number of T's = 18,730,641 bp (31.53%) number of G's = 13,958,364 bp (23.5%) number of N's = 2,941 bp (0%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 484,120 number of insertions = 5,045 mapped reads with insertion percentage = 0.54% number of deletions = 19,241 mapped reads with deletion percentage = 2.04% homopolymer indels = 48.56% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 0.197X There is a 1.76% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4942042 0.01982760155289643 0.2566289888975384 chr2 243199373 5582648 0.0229550262861903 0.25654185036334715 chr3 198022430 4774574 0.02411127870716464 0.16831210852816392 chr4 191154276 3247292 0.016987807272488113 0.14343682494193005 chr5 180915260 2977923 0.01646031959935276 0.1382768425631063 chr6 171115067 3177800 0.018571129098760193 0.16716162426864 chr7 159138663 3151462 0.019803245425029113 0.28153828806946174 chr8 146364022 4323038 0.02953620665056608 0.23535446736462445 chr9 141213431 2005173 0.014199591255593811 0.19539863156872198 chr10 135534747 3262228 0.02406931117080995 0.2055602775741421 chr11 135006516 2650751 0.019634244913038123 0.20455716954106284 chr12 133851895 2654369 0.01983064191956341 0.15415564682544391 chr13 115169878 1862051 0.016167864656416498 0.1380687535994705 chr14 107349540 2033648 0.018944170603805103 0.1531534977595728 chr15 102531392 1527090 0.014893877574587109 0.13459118698170236 chr16 90354753 1378547 0.015257050174217177 0.1418012992305981 chr17 81195210 1537789 0.018939405415664298 0.17017489628087218 chr18 78077248 1175287 0.015052874302127043 0.32176534185159084 chr19 59128983 946150 0.016001459047587544 0.192717295284078 chr20 63025520 1249266 0.019821589730636097 0.1529702565776334 chr21 48129895 661201 0.013737844223429118 0.1284035156204356 chr22 51304566 593014 0.011558698303772806 0.11431021220429843 chrMT 16571 14839 0.8954800555186772 1.1926820621217387 chrX 155270560 3555264 0.022897218893266052 0.1777986371987996 chrY 59373566 152607 0.0025702852343414914 0.06488680287446721