BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714219.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 215,582 number of mapped reads = 17,118 (7.94%) number of supplementary alignments = 544 (0.25%) number of secondary alignments = 0 number of mapped bases = 1,767,945 bp number of sequenced bases = 1,741,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,083 duplication rate = 39.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.5738 >>>>>>> ACTG content number of A's = 319,454 bp (18.34%) number of C's = 227,344 bp (13.06%) number of T's = 286,585 bp (16.46%) number of G's = 907,919 bp (52.14%) number of N's = 72 bp (0%) GC percentage = 65.19% >>>>>>> Mismatches and indels general error rate = 0.0379 number of mismatches = 57,509 number of insertions = 1,763 mapped reads with insertion percentage = 8.39% number of deletions = 4,096 mapped reads with deletion percentage = 22.68% homopolymer indels = 36.97% >>>>>>> Coverage mean coverageData = 0.0006X std coverageData = 0.7916X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 50389 2.021619837809752E-4 0.08420716848465537 chr2 243199373 765683 0.0031483757155903523 2.79694984619551 chr3 198022430 29091 1.469076003157824E-4 0.056397064736945016 chr4 191154276 44787 2.3429766227149425E-4 0.08741114209917257 chr5 180915260 40059 2.214241076181191E-4 0.06459213822904639 chr6 171115067 45239 2.6437765413141553E-4 0.07814570982248734 chr7 159138663 41936 2.6351861458079486E-4 0.08381386259759252 chr8 146364022 64480 4.405454231095125E-4 0.13324044194150134 chr9 141213431 43892 3.1082029300739814E-4 0.13440285939700533 chr10 135534747 24282 1.791570098256796E-4 0.049300371403733986 chr11 135006516 40866 3.026965009599981E-4 0.08967428663252508 chr12 133851895 30129 2.25092069111162E-4 0.07365823682059051 chr13 115169878 14525 1.2611804624816915E-4 0.05073819324801856 chr14 107349540 14659 1.3655391536843102E-4 0.04549751562981088 chr15 102531392 21967 2.1424657923302162E-4 0.07252118532765144 chr16 90354753 21063 2.3311446604253348E-4 0.07865159982173398 chr17 81195210 14638 1.8028157079709505E-4 0.05086940925766106 chr18 78077248 15532 1.9893119183708933E-4 0.04327259837668848 chr19 59128983 8811 1.4901321742672287E-4 0.05810455614140748 chr20 63025520 47262 7.498867125570721E-4 0.24768039385983584 chr21 48129895 3262 6.777492450378294E-5 0.01732699402302086 chr22 51304566 2843 5.5414171128550236E-5 0.015366075597453054 chrMT 16571 3412 0.20590187677267516 1.6588566862194862 chrX 155270560 372780 0.002400841473103465 0.3287507420169334 chrY 59373566 6358 1.0708469152753938E-4 0.05034934093170029