BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238606.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 = 3,616,625 number of mapped reads = 3,052,648 (84.41%) number of supplementary alignments = 24,788 (0.69%) number of secondary alignments = 0 number of mapped bases = 186,938,942 bp number of sequenced bases = 186,860,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 875,895 duplication rate = 20.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5769 >>>>>>> ACTG content number of A's = 46,429,803 bp (24.85%) number of C's = 32,049,830 bp (17.15%) number of T's = 63,765,755 bp (34.12%) number of G's = 44,611,118 bp (23.87%) number of N's = 4,303 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,023,358 number of insertions = 11,784 mapped reads with insertion percentage = 0.38% number of deletions = 46,098 mapped reads with deletion percentage = 1.5% homopolymer indels = 41.97% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.9145X There is a 2.82% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 10928495 0.04384540730993806 0.4459331814983083 chr2 243199373 9743701 0.04006466332460487 2.0296696344657197 chr3 198022430 24659954 0.12453111498530747 0.6797622139997828 chr4 191154276 6480777 0.03390338492872637 0.3532663608474672 chr5 180915260 3298334 0.01823137528586588 0.25987760498888435 chr6 171115067 28063207 0.16400196366109596 1.488366792249577 chr7 159138663 18119345 0.11385884899636238 1.6308129830263922 chr8 146364022 14635903 0.09999658932575657 0.8535412912450957 chr9 141213431 5407195 0.03829093990358467 0.4225528910734424 chr10 135534747 5609936 0.0413911275460602 0.4983709607724895 chr11 135006516 4194637 0.031069885545376194 0.33082457039155605 chr12 133851895 5832986 0.04357791124287034 0.4017097001701871 chr13 115169878 1710459 0.014851617712054883 0.44261383351826566 chr14 107349540 1825620 0.017006314139771814 0.25768207203999377 chr15 102531392 3131405 0.030540939110628676 0.4878460489459483 chr16 90354753 8067753 0.0892897466058039 0.6245990770814325 chr17 81195210 1289684 0.01588374486623041 0.2300190688695381 chr18 78077248 2917112 0.03736187013148824 1.5307587321437621 chr19 59128983 2633238 0.04453379487348869 0.45265952543496585 chr20 63025520 3488448 0.05534976942673381 0.4517418736047536 chr21 48129895 4024782 0.08362332807914914 0.5736397564226988 chr22 51304566 531690 0.010363405081723136 0.17658171061360967 chrMT 16571 80107 4.834168125037716 4.509347830239842 chrX 155270560 19614933 0.1263274441722887 0.6876618248209623 chrY 59373566 649241 0.010934849357035419 0.3322806808734215