BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240200.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 = 1,975,038 number of mapped reads = 1,470,062 (74.43%) number of supplementary alignments = 6,078 (0.31%) number of secondary alignments = 0 number of mapped bases = 91,367,320 bp number of sequenced bases = 91,317,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,940 duplication rate = 5.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.327 >>>>>>> ACTG content number of A's = 24,789,085 bp (27.15%) number of C's = 15,682,478 bp (17.17%) number of T's = 29,703,850 bp (32.53%) number of G's = 21,120,761 bp (23.13%) number of N's = 21,438 bp (0.02%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 847,228 number of insertions = 6,374 mapped reads with insertion percentage = 0.43% number of deletions = 28,990 mapped reads with deletion percentage = 1.95% homopolymer indels = 48.47% >>>>>>> Coverage mean coverageData = 0.0295X std coverageData = 0.2856X There is a 2.39% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.08% 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% 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 6620017 0.0265596810689591 0.40068252885779515 chr2 243199373 9038530 0.03716510403996806 0.34860173254440513 chr3 198022430 6554465 0.03309960896853957 0.21878761977384056 chr4 191154276 6087207 0.03184447205355741 0.22291683379960425 chr5 180915260 4892126 0.02704098040154269 0.1985323276616832 chr6 171115067 5292061 0.03092691422667064 0.26478399010811376 chr7 159138663 5588911 0.03511975590746291 0.45702374441131804 chr8 146364022 5398473 0.036883879837628405 0.4073024202245475 chr9 141213431 3304736 0.023402419844894214 0.250673484605242 chr10 135534747 4169848 0.030765896512132053 0.256715992410587 chr11 135006516 4205388 0.03114951873878443 0.27232622919303023 chr12 133851895 4338977 0.03241625380051586 0.21866039257504696 chr13 115169878 2061737 0.017901703429780483 0.1592377870352194 chr14 107349540 3444333 0.03208521433813317 0.2231504697257474 chr15 102531392 2047026 0.01996487085633247 0.1848012274925337 chr16 90354753 2658238 0.029420012912879084 0.21035841771670152 chr17 81195210 2286177 0.028156550121614318 0.2130818443538257 chr18 78077248 2250868 0.028828731258560752 0.40224240646269327 chr19 59128983 1604554 0.02713650596696378 0.31106773694519724 chr20 63025520 1976895 0.031366579760071796 0.21393722133838064 chr21 48129895 1669235 0.03468187495526429 0.23189324722413368 chr22 51304566 786105 0.01532232043440344 0.14339767952762367 chrMT 16571 34162 2.0615533160340354 2.4954571348883277 chrX 155270560 4864893 0.03133171542628557 0.2290232605865074 chrY 59373566 192358 0.003239791930301104 0.07220115827152093