BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472525.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 = 17,095,520 number of mapped reads = 16,745,260 (97.95%) number of supplementary alignments = 168,503 (0.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,484,651 number of mapped paired reads (second in pair) = 8,260,609 number of mapped paired reads (both in pair) = 16,476,408 number of mapped paired reads (singletons) = 268,852 number of mapped bases = 1,619,667,604 bp number of sequenced bases = 1,619,424,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,618,342 duplication rate = 43.59% >>>>>>> Insert size mean insert size = 206,333.6391 std insert size = 4,510,883.4129 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 51.8342 >>>>>>> ACTG content number of A's = 449,384,685 bp (27.75%) number of C's = 347,035,816 bp (21.43%) number of T's = 478,124,714 bp (29.52%) number of G's = 344,640,094 bp (21.28%) number of N's = 238,728 bp (0.01%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 11,012,520 number of insertions = 129,176 mapped reads with insertion percentage = 0.76% number of deletions = 96,900 mapped reads with deletion percentage = 0.57% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.5232X std coverageData = 21.2972X There is a 5.89% of reference with a coverageData >= 1X There is a 2.56% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 144804696 0.5809602215594881 19.543011217937387 chr2 243199373 122906581 0.5053737576864559 15.971969948920057 chr3 198022430 224598161 1.1342056604395774 23.52115544408169 chr4 191154276 55949068 0.29269064323729804 12.15430016726722 chr5 180915260 99823054 0.5517669100992365 22.56715732300528 chr6 171115067 103293480 0.60364923914035 29.918201728890544 chr7 159138663 37449089 0.23532363722321833 17.54497945045717 chr8 146364022 87333809 0.596689048350967 19.04330168909842 chr9 141213431 100924878 0.7146974426249866 18.53915843956102 chr10 135534747 25515342 0.18825683129065052 11.317900848619537 chr11 135006516 60371532 0.447174949689095 18.943233651325627 chr12 133851895 85713074 0.6403575683407396 40.19376481916423 chr13 115169878 15239425 0.13232127414426886 6.589466769527734 chr14 107349540 58853938 0.5482458331912741 21.17702548124201 chr15 102531392 63236207 0.6167497170037446 30.407494303545064 chr16 90354753 66108698 0.7316571160346153 27.278691276536527 chr17 81195210 71225871 0.8772176462133665 23.756577477171724 chr18 78077248 39213965 0.5022457374522217 17.8575216609463 chr19 59128983 28253626 0.47783040679052435 13.125513036745385 chr20 63025520 40372275 0.6405702801024094 30.53051206874231 chr21 48129895 9386827 0.19503111319897956 7.682975536537405 chr22 51304566 17448055 0.34008776138950286 13.164965407171712 chrMT 16571 4956622 299.1142357129926 904.3264331293082 chrX 155270560 52446911 0.33777756066571796 16.143006457417734 chrY 59373566 4242420 0.07145300991353627 12.239329957687062