BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174067.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 = 8,518,992 number of mapped reads = 8,323,014 (97.7%) number of supplementary alignments = 837,459 (9.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,155,524 number of mapped paired reads (second in pair) = 4,167,490 number of mapped paired reads (both in pair) = 8,192,346 number of mapped paired reads (singletons) = 130,668 number of mapped bases = 990,646,597 bp number of sequenced bases = 990,109,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,592,779 duplication rate = 66.72% >>>>>>> Insert size mean insert size = 960,473.8683 std insert size = 9,149,372.2841 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.8306 >>>>>>> ACTG content number of A's = 296,570,036 bp (29.95%) number of C's = 195,313,017 bp (19.73%) number of T's = 296,143,475 bp (29.91%) number of G's = 202,070,953 bp (20.41%) number of N's = 12,304 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 9,990,141 number of insertions = 105,060 mapped reads with insertion percentage = 1.22% number of deletions = 217,908 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.31% >>>>>>> Coverage mean coverageData = 0.32X std coverageData = 4.302X There is a 6.34% of reference with a coverageData >= 1X There is a 5.1% of reference with a coverageData >= 2X There is a 4.02% of reference with a coverageData >= 3X There is a 3.33% of reference with a coverageData >= 4X There is a 2.57% of reference with a coverageData >= 5X There is a 2.09% of reference with a coverageData >= 6X There is a 1.57% of reference with a coverageData >= 7X There is a 1.28% of reference with a coverageData >= 8X There is a 0.96% of reference with a coverageData >= 9X There is a 0.8% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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% 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 76592307 0.3072903356978998 2.6180323385866027 chr2 243199373 92542010 0.3805191142495256 13.283851345586372 chr3 198022430 75048188 0.3789883196565157 1.8394735520412622 chr4 191154276 55684628 0.2913072580181256 1.9773405400496527 chr5 180915260 59108944 0.32672171490674695 1.678020575656326 chr6 171115067 48048608 0.28079706154689466 1.957399932567933 chr7 159138663 63060840 0.3962634774680745 2.727535923218004 chr8 146364022 49263685 0.33658329640599793 2.4705293772203323 chr9 141213431 37458313 0.2652602711706651 2.2851728594874774 chr10 135534747 56677112 0.4181740347366421 3.911513353720395 chr11 135006516 36148840 0.2677562614829643 1.5657430368459901 chr12 133851895 48553288 0.3627388913694498 1.7737455844190575 chr13 115169878 25608805 0.22235679541138353 1.3914933672461474 chr14 107349540 30628149 0.2853123450738587 1.5697609289511578 chr15 102531392 24939916 0.24324175760727018 1.4370882756299999 chr16 90354753 36052171 0.39900691223183354 2.66838174231104 chr17 81195210 41594345 0.5122758473067561 2.5266803784546394 chr18 78077248 19592447 0.2509367005353467 3.3233734601245732 chr19 59128983 14787579 0.2500901968836501 2.2442884177582414 chr20 63025520 44842814 0.7115024834384548 2.8312301025588846 chr21 48129895 13237636 0.2750397855636294 1.6619614951654604 chr22 51304566 8497162 0.16562194483820408 1.1491783516239438 chrMT 16571 1823760 110.05732906885522 99.4262101687207 chrX 155270560 28333394 0.182477566899997 1.2495808509293553 chrY 59373566 2521656 0.04247102153170318 1.1906941866857976