BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173986.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,473,178 number of mapped reads = 2,416,355 (97.7%) number of supplementary alignments = 308,332 (12.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,208,534 number of mapped paired reads (second in pair) = 1,207,821 number of mapped paired reads (both in pair) = 2,380,936 number of mapped paired reads (singletons) = 35,419 number of mapped bases = 274,808,851 bp number of sequenced bases = 274,625,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,923,248 duplication rate = 64.64% >>>>>>> Insert size mean insert size = 1,181,363.0245 std insert size = 10,292,660.7632 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.5501 >>>>>>> ACTG content number of A's = 81,623,704 bp (29.72%) number of C's = 54,890,936 bp (19.99%) number of T's = 81,040,415 bp (29.51%) number of G's = 57,068,974 bp (20.78%) number of N's = 1,845 bp (0%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,316,636 number of insertions = 29,914 mapped reads with insertion percentage = 1.19% number of deletions = 76,174 mapped reads with deletion percentage = 3.08% homopolymer indels = 41.86% >>>>>>> Coverage mean coverageData = 0.0888X std coverageData = 1.7471X There is a 1.95% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.87% of reference with a coverageData >= 4X There is a 0.65% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 21974096 0.08816064694980238 1.0401682377761854 chr2 243199373 24769487 0.10184848215048646 5.263492519813231 chr3 198022430 17040976 0.08605578671062666 0.8737716294574095 chr4 191154276 17849915 0.09337962704009822 1.0342493085324957 chr5 180915260 15852412 0.0876234099876373 0.87852796422746 chr6 171115067 16551537 0.09672752546098118 0.9729217454478244 chr7 159138663 15304516 0.09617094747113716 1.082366910132997 chr8 146364022 14744542 0.10073884140735077 1.2524246552068097 chr9 141213431 11804697 0.08359471840890262 0.9379857830727243 chr10 135534747 13745621 0.10141769032851775 1.2049875858097148 chr11 135006516 12946110 0.09589248270061276 0.9417955646674864 chr12 133851895 12668606 0.0946464448635561 0.9280870383323365 chr13 115169878 8563883 0.07435870514684403 0.8180717615548779 chr14 107349540 8880647 0.08272645602393824 0.8697990845090561 chr15 102531392 8253596 0.08049823414081807 0.843961474168593 chr16 90354753 8867985 0.09814630338262338 1.0041429061515865 chr17 81195210 8141846 0.10027495464326036 0.959557922551721 chr18 78077248 7756340 0.09934187229549894 1.2052347281864173 chr19 59128983 5412775 0.0915418247596107 0.9351078351295727 chr20 63025520 6034134 0.09574112200898938 0.9320859783177914 chr21 48129895 3828237 0.07953969149527544 0.9865416249906575 chr22 51304566 3432793 0.06691008749591605 0.8513690780398293 chrMT 16571 354617 21.399855168668154 19.166468830228034 chrX 155270560 7826712 0.0504069283964713 0.6662763899329643 chrY 59373566 2202771 0.03710019708097034 0.6845099680705157