BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234071.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 = 4,605,264 number of mapped reads = 4,339,247 (94.22%) number of supplementary alignments = 30,167 (0.66%) number of secondary alignments = 0 number of mapped bases = 279,171,518 bp number of sequenced bases = 279,064,278 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 477,114 duplication rate = 9.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3785 >>>>>>> ACTG content number of A's = 72,052,964 bp (25.82%) number of C's = 50,237,354 bp (18%) number of T's = 90,972,125 bp (32.6%) number of G's = 65,775,419 bp (23.57%) number of N's = 26,416 bp (0.01%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,530,376 number of insertions = 17,939 mapped reads with insertion percentage = 0.41% number of deletions = 62,211 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0902X std coverageData = 1.0071X There is a 6.89% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23043474 0.09245101940989747 2.2051163530759714 chr2 243199373 12403970 0.05100329761129771 1.7522560687375794 chr3 198022430 39598703 0.19997079623757774 0.5650665186420895 chr4 191154276 10698817 0.05596954054012373 0.3400806364533774 chr5 180915260 20879943 0.11541283471609858 0.4392209455718158 chr6 171115067 12945152 0.07565173673455652 0.5619899832190058 chr7 159138663 18560572 0.11663144361090931 1.214704993269548 chr8 146364022 15038571 0.10274772990318617 1.1802728302149874 chr9 141213431 7080507 0.05014046433019533 0.5821278101400105 chr10 135534747 11611658 0.08567292341645792 0.5992325973512334 chr11 135006516 11280716 0.08355682624977893 0.6601958342303743 chr12 133851895 4520060 0.033769114736851506 0.27297692580191546 chr13 115169878 11505977 0.09990439514054186 0.4487454917257459 chr14 107349540 14872879 0.13854627602503 0.49077664843883395 chr15 102531392 5985392 0.058376189801461004 0.3398398771330875 chr16 90354753 7807768 0.08641236615410813 0.43729911062697063 chr17 81195210 8257858 0.10170375814041246 0.4667016211379208 chr18 78077248 6336413 0.08115569083582454 1.4089975170185478 chr19 59128983 9808751 0.16588736187125017 1.2219167542947345 chr20 63025520 9572509 0.15188306260702014 0.5117247141226294 chr21 48129895 3613837 0.07508507965787169 0.3702221052669387 chr22 51304566 3370787 0.06570150111005714 0.3130156586411414 chrMT 16571 102224 6.168849194375716 4.049029660898583 chrX 155270560 9637093 0.06206645355049921 0.41002879536162645 chrY 59373566 637887 0.01074361947537394 0.2312692532650147