BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354847.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 22,880,488 number of mapped reads = 22,680,210 (99.12%) number of supplementary alignments = 551,858 (2.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,351,134 number of mapped paired reads (second in pair) = 11,329,076 number of mapped paired reads (both in pair) = 22,631,262 number of mapped paired reads (singletons) = 48,948 number of mapped bases = 2,963,296,657 bp number of sequenced bases = 2,961,722,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,259,334 duplication rate = 39.62% >>>>>>> Insert size mean insert size = 224,768.3306 std insert size = 5,432,509.5286 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 53.9013 >>>>>>> ACTG content number of A's = 837,620,591 bp (28.28%) number of C's = 628,233,808 bp (21.21%) number of T's = 848,897,954 bp (28.66%) number of G's = 646,934,659 bp (21.84%) number of N's = 35,119 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 22,795,686 number of insertions = 532,917 mapped reads with insertion percentage = 2.19% number of deletions = 563,265 mapped reads with deletion percentage = 2.37% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.9572X std coverageData = 25.0348X There is a 36.41% of reference with a coverageData >= 1X There is a 25.01% of reference with a coverageData >= 2X There is a 11.61% of reference with a coverageData >= 3X There is a 7.86% of reference with a coverageData >= 4X There is a 3.63% of reference with a coverageData >= 5X There is a 2.41% of reference with a coverageData >= 6X There is a 1.14% of reference with a coverageData >= 7X There is a 0.75% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 242816027 0.9741842408488924 26.216817542291714 chr2 243199373 267102937 1.0982879343196332 76.98945438562522 chr3 198022430 192870199 0.9739815787534776 2.155974809025847 chr4 191154276 196745286 1.0292486786955266 13.56066259913408 chr5 180915260 174615024 0.9651757623983737 1.7389326357583603 chr6 171115067 166681474 0.9740899905675752 3.8875780246794127 chr7 159138663 161200854 1.012958453722839 15.225445163223139 chr8 146364022 144797079 0.9892942064683081 3.60605495390634 chr9 141213431 126736654 0.8974830021657076 14.069283620501235 chr10 135534747 166594536 1.2291647690905418 33.61515767381506 chr11 135006516 135832832 1.0061205638400446 4.887437973966691 chr12 133851895 130165232 0.9724571475062045 1.8565442559988439 chr13 115169878 89487775 0.7770067708155426 1.4978566193451013 chr14 107349540 88561053 0.8249784116448007 3.698216471009357 chr15 102531392 84826604 0.8273232455480561 1.5416312451808072 chr16 90354753 93978344 1.0401040441115477 5.993111738757779 chr17 81195210 85729934 1.0558496492588665 6.0602292445569335 chr18 78077248 80163539 1.0267208572720186 12.238558465824916 chr19 59128983 62636172 1.05931421144179 12.921930270811291 chr20 63025520 63740692 1.0113473399346804 4.495807958040366 chr21 48129895 40799837 0.8477025973150367 7.261708992673946 chr22 51304566 38180814 0.7441991420412756 2.960303171387133 chrMT 16571 13819065 833.9306619998794 171.60374054789406 chrX 155270560 79011738 0.5088649000815093 2.1354990274390904 chrY 59373566 36202956 0.6097487221838755 17.300464198778197