BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068189.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 = 1,592,272 number of mapped reads = 1,409,855 (88.54%) number of supplementary alignments = 9,791 (0.61%) number of secondary alignments = 0 number of mapped bases = 94,724,636 bp number of sequenced bases = 94,683,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,482 duplication rate = 7.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9073 >>>>>>> ACTG content number of A's = 27,138,210 bp (28.66%) number of C's = 17,194,178 bp (18.16%) number of T's = 30,375,386 bp (32.08%) number of G's = 19,872,281 bp (20.99%) number of N's = 103,165 bp (0.11%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 841,158 number of insertions = 7,126 mapped reads with insertion percentage = 0.5% number of deletions = 23,544 mapped reads with deletion percentage = 1.65% homopolymer indels = 48.42% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.6038X There is a 1.73% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 15038690 0.060335616977259206 1.5396238202547208 chr2 243199373 4439688 0.018255343117188055 0.34024002931862457 chr3 198022430 2384561 0.012041873236279345 0.16878447805463073 chr4 191154276 8264899 0.04323679895081186 0.3402880599966344 chr5 180915260 9314845 0.05148733722075186 0.3671197618840373 chr6 171115067 3211151 0.01876603303436745 0.3598122900904099 chr7 159138663 10472025 0.06580440480387849 0.6233796494827128 chr8 146364022 2086268 0.014253967412838655 0.6698776907286811 chr9 141213431 1768523 0.01252375915999095 0.45483391033764003 chr10 135534747 1787563 0.01318896474569728 0.2508484121017586 chr11 135006516 1712418 0.012683965565039838 0.3018781597587196 chr12 133851895 1886083 0.01409082030553247 0.26388930340458067 chr13 115169878 4183386 0.036323612325090765 0.3070891188476947 chr14 107349540 9669068 0.09007088432796265 0.5439203308844133 chr15 102531392 1067454 0.010410996858406059 0.15733770819056123 chr16 90354753 7300503 0.08079821766542818 0.5898003216222263 chr17 81195210 1302603 0.016042855237396392 0.19799246733923853 chr18 78077248 1638576 0.020986600347389292 0.975931643137405 chr19 59128983 916476 0.015499607020130889 1.0922250972252707 chr20 63025520 912554 0.014479118934679158 0.26685801312572277 chr21 48129895 2670733 0.05549010651280249 0.37604506916082703 chr22 51304566 427418 0.00833099338565694 0.13437495683974235 chrMT 16571 53952 3.2558083398708586 3.456723876187265 chrX 155270560 2029248 0.01306910981708316 0.23475349797622644 chrY 59373566 185951 0.0031318819556837804 0.111061107603182