BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695972.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 60,544,978 number of mapped reads = 60,188,225 (99.41%) number of supplementary alignments = 597,319 (0.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,186,623 number of mapped paired reads (second in pair) = 30,001,602 number of mapped paired reads (both in pair) = 59,934,144 number of mapped paired reads (singletons) = 254,081 number of mapped bases = 5,972,523,738 bp number of sequenced bases = 5,971,232,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,822,551 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 73,018.7278 std insert size = 2,597,404.0169 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.9109 >>>>>>> ACTG content number of A's = 1,768,689,955 bp (29.62%) number of C's = 1,200,903,330 bp (20.11%) number of T's = 1,759,312,004 bp (29.46%) number of G's = 1,235,838,911 bp (20.7%) number of N's = 6,488,499 bp (0.11%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 38,551,101 number of insertions = 557,293 mapped reads with insertion percentage = 0.91% number of deletions = 563,416 mapped reads with deletion percentage = 0.92% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 1.9293X std coverageData = 2.7925X There is a 72.28% of reference with a coverageData >= 1X There is a 48.93% of reference with a coverageData >= 2X There is a 30.14% of reference with a coverageData >= 3X There is a 17.55% of reference with a coverageData >= 4X There is a 9.9% of reference with a coverageData >= 5X There is a 5.52% of reference with a coverageData >= 6X There is a 3.07% of reference with a coverageData >= 7X There is a 1.73% of reference with a coverageData >= 8X There is a 0.99% of reference with a coverageData >= 9X There is a 0.58% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.15% 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 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% 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 0.03% 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 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 486609946 1.952291809936955 2.900813607824925 chr2 243199373 553904145 2.277572257556766 2.6951932203750513 chr3 198022430 433487028 2.1890804390189538 2.0288091775885246 chr4 191154276 401903505 2.1025085779404695 2.510909536329369 chr5 180915260 424121172 2.3443084458436507 2.128120250189475 chr6 171115067 363408876 2.123769007436382 2.3447115046984512 chr7 159138663 323497400 2.0328020476080035 2.1043682946652527 chr8 146364022 306306317 2.092770564886499 2.05560365049422 chr9 141213431 248470376 1.759537844526984 2.3442089372882733 chr10 135534747 275876184 2.035464632549172 3.0802352319165562 chr11 135006516 282305540 2.0910512200759257 2.121887112069265 chr12 133851895 283642526 2.119077402677041 2.1120880680275715 chr13 115169878 194091207 1.6852601597789312 1.9283161100815525 chr14 107349540 191889689 1.7875222287864485 2.0395901398214513 chr15 102531392 183559560 1.7902766793607952 2.1214286425778552 chr16 90354753 144945015 1.6041769822557093 2.6637162402202 chr17 81195210 135289352 1.6662233153901567 2.3483120016286256 chr18 78077248 161865320 2.0731432542294526 2.9852699683129207 chr19 59128983 80946081 1.3689746870836592 2.090456350892682 chr20 63025520 111897372 1.7754295720209845 2.09413834476232 chr21 48129895 77222456 1.6044592659094727 3.2842396948556196 chr22 51304566 58589572 1.1419952758200898 1.7767419780897662 chrMT 16571 10041051 605.9411622714381 164.1495666228392 chrX 155270560 200512797 1.2913767877181612 1.493277858281454 chrY 59373566 38141251 0.6423944790515025 2.529690930098487