BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237274.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 = 2,965,445 number of mapped reads = 2,683,014 (90.48%) number of supplementary alignments = 13,955 (0.47%) number of secondary alignments = 0 number of mapped bases = 181,551,596 bp number of sequenced bases = 181,462,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,385 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6246 >>>>>>> ACTG content number of A's = 51,655,862 bp (28.47%) number of C's = 33,614,629 bp (18.52%) number of T's = 56,860,053 bp (31.33%) number of G's = 39,329,161 bp (21.67%) number of N's = 3,149 bp (0%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,408,230 number of insertions = 13,561 mapped reads with insertion percentage = 0.5% number of deletions = 50,621 mapped reads with deletion percentage = 1.87% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.5628X There is a 4.63% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20898954 0.08384714917119504 0.8038437349346502 chr2 243199373 13465161 0.055366758696372136 0.6536630671585444 chr3 198022430 13285664 0.06709171279233368 0.3092463710359715 chr4 191154276 6909671 0.036147090949720635 0.2493735242376102 chr5 180915260 7546042 0.04171036760525342 0.2500006865346134 chr6 171115067 25177184 0.14713598540098166 0.8024101074429377 chr7 159138663 12802713 0.08045004751610864 1.0385025065802165 chr8 146364022 6144191 0.04197883411539483 0.8305406029412572 chr9 141213431 8225821 0.05825098180639772 0.5756703084947331 chr10 135534747 6741276 0.04973835971376403 0.47427613742845165 chr11 135006516 5949022 0.0440647027733091 0.39305095112197497 chr12 133851895 8123719 0.06069184900221248 0.3088851588158583 chr13 115169878 6238499 0.054167800716086546 0.28057983711760004 chr14 107349540 6973749 0.0649630077595116 0.35474231606780054 chr15 102531392 4082217 0.03981431364942358 0.2429133710143824 chr16 90354753 3457626 0.03826722873117699 0.3002076027378172 chr17 81195210 2987680 0.036796259286723934 0.3100377845562733 chr18 78077248 4986406 0.06386503274295734 1.0596662657962002 chr19 59128983 2723949 0.04606791562777259 0.5201829707107417 chr20 63025520 3244933 0.051486017092758615 0.2849446276247361 chr21 48129895 3749796 0.07790991440974471 0.367535213041693 chr22 51304566 1637108 0.03190959650647859 0.21122392737637555 chrMT 16571 130637 7.883471124253213 5.0617661431083505 chrX 155270560 5746071 0.03700682859648345 0.28591533326003005 chrY 59373566 323507 0.005448670541365159 0.14158023851528412