BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038429.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,639,096 number of mapped reads = 17,670,287 (94.8%) number of supplementary alignments = 318,466 (1.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,939,882 number of mapped paired reads (second in pair) = 8,730,405 number of mapped paired reads (both in pair) = 17,397,032 number of mapped paired reads (singletons) = 273,255 number of mapped bases = 2,368,854,559 bp number of sequenced bases = 2,367,083,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,783,581 duplication rate = 14.79% >>>>>>> Insert size mean insert size = 75,643.0929 std insert size = 2,620,104.012 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 53.4652 >>>>>>> ACTG content number of A's = 673,703,760 bp (28.46%) number of C's = 473,081,862 bp (19.99%) number of T's = 685,859,330 bp (28.97%) number of G's = 534,251,602 bp (22.57%) number of N's = 186,582 bp (0.01%) GC percentage = 42.56% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 30,536,999 number of insertions = 454,863 mapped reads with insertion percentage = 2.42% number of deletions = 849,130 mapped reads with deletion percentage = 4.61% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.7652X std coverageData = 10.504X There is a 28.29% of reference with a coverageData >= 1X There is a 16.78% of reference with a coverageData >= 2X There is a 9.55% of reference with a coverageData >= 3X There is a 6% of reference with a coverageData >= 4X There is a 3.71% of reference with a coverageData >= 5X There is a 2.4% of reference with a coverageData >= 6X There is a 1.55% of reference with a coverageData >= 7X There is a 1.04% of reference with a coverageData >= 8X There is a 0.7% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% 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 0.04% 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 0.01% 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 188641274 0.7568337171765762 16.619515442785662 chr2 243199373 210463228 0.8653937935933741 11.429256291960929 chr3 198022430 157376401 0.7947402776544051 1.758665322244069 chr4 191154276 155261448 0.8122311007052754 12.585808110236563 chr5 180915260 138183633 0.7638030810667934 1.7119157565121716 chr6 171115067 139587752 0.8157537173509098 7.270429238242288 chr7 159138663 123774567 0.7777781003476195 9.695627092283694 chr8 146364022 116796293 0.7979849925140756 3.5328086211923897 chr9 141213431 97486445 0.6903482502312404 16.437375709204048 chr10 135534747 129904423 0.9584584460839404 23.985298945135014 chr11 135006516 110044936 0.8151083315119397 6.531644282343905 chr12 133851895 101466337 0.7580493126376732 1.8092887966533127 chr13 115169878 69699224 0.6051862276002411 1.4753590884475767 chr14 107349540 67322030 0.6271291893751944 1.7319800754229957 chr15 102531392 65611093 0.639912242681734 1.5583741147953307 chr16 90354753 79241036 0.8769990882494029 12.916460391035669 chr17 81195210 62332486 0.7676867391561645 12.413292211076561 chr18 78077248 65455960 0.838348708192174 13.090037076637216 chr19 59128983 35158055 0.5945993524021883 7.683311409417909 chr20 63025520 50285058 0.7978523302941412 4.075711890098996 chr21 48129895 31281086 0.6499304849927472 5.618364402071958 chr22 51304566 23818392 0.46425481895704956 1.440207972033019 chrMT 16571 3061540 184.75288154003982 113.98979096413431 chrX 155270560 137103557 0.8829977620999113 3.535209850033285 chrY 59373566 9498305 0.15997531628805992 13.39694901764207