BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173989.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,949,354 number of mapped reads = 10,710,453 (97.82%) number of supplementary alignments = 1,401,179 (12.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,360,264 number of mapped paired reads (second in pair) = 5,350,189 number of mapped paired reads (both in pair) = 10,561,932 number of mapped paired reads (singletons) = 148,521 number of mapped bases = 1,213,976,992 bp number of sequenced bases = 1,213,137,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,611,658 duplication rate = 65.03% >>>>>>> Insert size mean insert size = 972,070.436 std insert size = 9,149,246.2791 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 52.586 >>>>>>> ACTG content number of A's = 364,204,005 bp (30.02%) number of C's = 239,528,676 bp (19.74%) number of T's = 360,991,366 bp (29.76%) number of G's = 248,404,540 bp (20.48%) number of N's = 9,057 bp (0%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 10,461,661 number of insertions = 132,939 mapped reads with insertion percentage = 1.2% number of deletions = 358,912 mapped reads with deletion percentage = 3.27% homopolymer indels = 40.9% >>>>>>> Coverage mean coverageData = 0.3922X std coverageData = 6.5874X There is a 8.13% of reference with a coverageData >= 1X There is a 6.15% of reference with a coverageData >= 2X There is a 4.61% of reference with a coverageData >= 3X There is a 3.74% of reference with a coverageData >= 4X There is a 2.83% of reference with a coverageData >= 5X There is a 2.37% of reference with a coverageData >= 6X There is a 1.79% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 1.06% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.73% of reference with a coverageData >= 12X There is a 0.55% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.38% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 99539200 0.39935386961382935 3.0488316177121297 chr2 243199373 109988505 0.45225653192781873 21.67772493301123 chr3 198022430 83268909 0.420502409752269 1.9872695858560885 chr4 191154276 83801230 0.438395790842785 3.0492872221483176 chr5 180915260 74442902 0.4114793964865098 1.9472338573140655 chr6 171115067 73600017 0.4301200256082651 2.5636350964561085 chr7 159138663 67432138 0.4237319626092372 2.9997813775153106 chr8 146364022 62971029 0.43023571052181114 3.579828817954252 chr9 141213431 51267109 0.3630469753263059 2.9284916032004715 chr10 135534747 59808194 0.44127572688057626 3.9743717488509036 chr11 135006516 53963647 0.3997114257803675 2.0486079897381155 chr12 133851895 54867098 0.4099090117476484 2.0949815233054894 chr13 115169878 39249734 0.3407986070802298 1.7835713077831097 chr14 107349540 37347312 0.34790379166971747 1.8460458549123515 chr15 102531392 35025348 0.34160609074730985 1.8693261033705177 chr16 90354753 37036270 0.40989841453055603 2.8196487372412684 chr17 81195210 33399247 0.4113450411668373 2.28126531998331 chr18 78077248 33965581 0.4350253354216583 3.9563413149063535 chr19 59128983 21913270 0.37060116525258013 2.361592809513148 chr20 63025520 26441501 0.41953641953291304 2.0987997138425594 chr21 48129895 17284738 0.35912685868107547 2.7537401910588537 chr22 51304566 14565248 0.2838976944079402 2.1992834031744533 chrMT 16571 1459888 88.0989680767606 68.061456258297 chrX 155270560 32073658 0.20656625441423024 1.4087816132939333 chrY 59373566 9265219 0.15604956252753963 2.425121226089382