BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038408.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 = 19,407,710 number of mapped reads = 18,772,648 (96.73%) number of supplementary alignments = 276,452 (1.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,481,565 number of mapped paired reads (second in pair) = 9,291,083 number of mapped paired reads (both in pair) = 18,535,020 number of mapped paired reads (singletons) = 237,628 number of mapped bases = 2,535,808,085 bp number of sequenced bases = 2,534,058,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,097,266 duplication rate = 15.36% >>>>>>> Insert size mean insert size = 66,757.1487 std insert size = 2,484,024.9255 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 53.4585 >>>>>>> ACTG content number of A's = 725,134,748 bp (28.62%) number of C's = 502,763,510 bp (19.84%) number of T's = 739,068,623 bp (29.17%) number of G's = 566,890,816 bp (22.37%) number of N's = 201,167 bp (0.01%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 30,981,628 number of insertions = 438,833 mapped reads with insertion percentage = 2.22% number of deletions = 883,068 mapped reads with deletion percentage = 4.53% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.8191X std coverageData = 12.0671X There is a 27.6% of reference with a coverageData >= 1X There is a 17.05% of reference with a coverageData >= 2X There is a 10.35% of reference with a coverageData >= 3X There is a 6.82% of reference with a coverageData >= 4X There is a 4.47% of reference with a coverageData >= 5X There is a 3.03% of reference with a coverageData >= 6X There is a 2.08% of reference with a coverageData >= 7X There is a 1.45% of reference with a coverageData >= 8X There is a 1.03% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.01% 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 209793520 0.8416970804658497 15.921343790871077 chr2 243199373 285113913 1.1723464147253373 15.123495217558752 chr3 198022430 179837808 0.9081688776367405 2.125731561782673 chr4 191154276 108825713 0.569308284790867 11.242458596100867 chr5 180915260 167882623 0.927962754496221 2.000451034922136 chr6 171115067 149422038 0.8732254886707317 10.705278983952446 chr7 159138663 118476972 0.7444889241026237 11.207141384282327 chr8 146364022 153136875 1.0462740290096701 4.439421949309719 chr9 141213431 106268549 0.7525385386323487 18.691758348252325 chr10 135534747 136729699 1.0088165730666838 32.79786740278486 chr11 135006516 112315283 0.8319249050171771 8.3158783636792 chr12 133851895 107035405 0.7996555073052944 2.013463261018147 chr13 115169878 84313036 0.7320754129825509 1.7236550958882424 chr14 107349540 81848533 0.7624488470094981 1.881155819627257 chr15 102531392 67165507 0.6550726142487171 1.65530784173629 chr16 90354753 80121806 0.886746998245903 12.473702432091523 chr17 81195210 58854934 0.7248572175624646 13.324802153140315 chr18 78077248 102140770 1.3082014622236686 13.447317195394454 chr19 59128983 31608576 0.534569924870854 6.565701162168893 chr20 63025520 62167285 0.9863827382939482 4.014337639372555 chr21 48129895 24241594 0.5036702033112684 5.073212469428886 chr22 51304566 13410862 0.2613970460251043 1.0141101556960253 chrMT 16571 4778784 288.38235471607027 151.53152526818738 chrX 155270560 84870946 0.546600372923238 2.5091268386044074 chrY 59373566 5447054 0.09174207255801345 11.137798036476566