BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472775.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,130,134 number of mapped reads = 19,877,213 (98.74%) number of supplementary alignments = 75,186 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,997,028 number of mapped paired reads (second in pair) = 9,880,185 number of mapped paired reads (both in pair) = 19,714,018 number of mapped paired reads (singletons) = 163,195 number of mapped bases = 1,959,010,966 bp number of sequenced bases = 1,958,706,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,989,837 duplication rate = 47.56% >>>>>>> Insert size mean insert size = 26,420.2233 std insert size = 1,588,667.2381 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 55.0801 >>>>>>> ACTG content number of A's = 549,941,828 bp (28.08%) number of C's = 431,938,566 bp (22.05%) number of T's = 546,752,812 bp (27.91%) number of G's = 429,697,409 bp (21.94%) number of N's = 376,313 bp (0.02%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 13,383,650 number of insertions = 119,805 mapped reads with insertion percentage = 0.6% number of deletions = 120,473 mapped reads with deletion percentage = 0.59% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.6328X std coverageData = 21.7861X There is a 5.36% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 213307868 0.8557967364101372 30.161993996512553 chr2 243199373 147545767 0.6066864613174805 27.889379415948195 chr3 198022430 233284775 1.1780724789610955 26.820718708040182 chr4 191154276 68925195 0.3605736499454503 12.507874524762324 chr5 180915260 96254992 0.5320446268601112 18.894783766553115 chr6 171115067 124371886 0.7268318809120415 24.146400637570892 chr7 159138663 104797561 0.6585298570718795 22.013174157660465 chr8 146364022 87595516 0.5984771038882766 19.928158846132515 chr9 141213431 102930610 0.7289009924275546 19.286309559430325 chr10 135534747 48203498 0.35565417036562585 12.774595849330938 chr11 135006516 77690933 0.5754606170268107 17.89314188207101 chr12 133851895 119539692 0.8930743341362481 25.960537629481728 chr13 115169878 44096068 0.3828784814723864 14.658487640947616 chr14 107349540 70949540 0.6609207640759336 28.343163546660392 chr15 102531392 45196991 0.4408112493001168 13.947005786643743 chr16 90354753 71840490 0.7950936460420627 21.663877125901028 chr17 81195210 100710088 1.240345187850367 38.096703800743654 chr18 78077248 38803838 0.49699290118422207 15.788331231435702 chr19 59128983 30735671 0.519807198442767 15.832302204373711 chr20 63025520 40379793 0.6406895651158452 16.838846097997486 chr21 48129895 9164595 0.19041377505602286 7.745404242444065 chr22 51304566 15617499 0.30440758430740844 9.058604461675486 chrMT 16571 6683 0.40329491279946894 1.1036333444143984 chrX 155270560 65226768 0.42008458010327265 12.091254950931933 chrY 59373566 1834649 0.030900097865100437 0.8604940497314334