BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975295.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 48,549,422 number of mapped reads = 48,438,374 (99.77%) number of supplementary alignments = 87,025 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,210,708 number of mapped paired reads (second in pair) = 24,227,666 number of mapped paired reads (both in pair) = 48,381,092 number of mapped paired reads (singletons) = 57,282 number of mapped bases = 4,450,583,873 bp number of sequenced bases = 4,448,997,548 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,407,938 duplication rate = 43.37% >>>>>>> Insert size mean insert size = 77,392.9758 std insert size = 2,753,533.5789 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 56.1109 >>>>>>> ACTG content number of A's = 1,191,679,756 bp (26.79%) number of C's = 979,507,824 bp (22.02%) number of T's = 1,207,354,066 bp (27.14%) number of G's = 1,070,317,354 bp (24.06%) number of N's = 138,548 bp (0%) GC percentage = 46.07% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 29,625,087 number of insertions = 436,862 mapped reads with insertion percentage = 0.89% number of deletions = 1,128,434 mapped reads with deletion percentage = 2.3% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 1.4377X std coverageData = 20.4089X There is a 11.45% of reference with a coverageData >= 1X There is a 5.8% of reference with a coverageData >= 2X There is a 3.41% of reference with a coverageData >= 3X There is a 2.64% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 1.94% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.67% of reference with a coverageData >= 8X There is a 1.58% of reference with a coverageData >= 9X There is a 1.5% of reference with a coverageData >= 10X There is a 1.44% of reference with a coverageData >= 11X There is a 1.39% of reference with a coverageData >= 12X There is a 1.34% of reference with a coverageData >= 13X There is a 1.29% of reference with a coverageData >= 14X There is a 1.25% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.14% of reference with a coverageData >= 18X There is a 1.11% of reference with a coverageData >= 19X There is a 1.08% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 1.03% of reference with a coverageData >= 22X There is a 1.01% of reference with a coverageData >= 23X There is a 0.98% of reference with a coverageData >= 24X There is a 0.96% of reference with a coverageData >= 25X There is a 0.94% of reference with a coverageData >= 26X There is a 0.92% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.88% of reference with a coverageData >= 29X There is a 0.86% of reference with a coverageData >= 30X There is a 0.85% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.82% of reference with a coverageData >= 33X There is a 0.8% of reference with a coverageData >= 34X There is a 0.79% of reference with a coverageData >= 35X There is a 0.77% of reference with a coverageData >= 36X There is a 0.76% of reference with a coverageData >= 37X There is a 0.74% of reference with a coverageData >= 38X There is a 0.73% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.69% of reference with a coverageData >= 42X There is a 0.68% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.66% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.64% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.61% of reference with a coverageData >= 50X There is a 0.6% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 509361572 2.0435719275499817 25.61728480547486 chr2 243199373 343221097 1.4112745965015296 18.469196862706806 chr3 198022430 297108613 1.5003785833756307 20.07329036108481 chr4 191154276 201294031 1.053044876694257 16.423862878089302 chr5 180915260 217765072 1.2036854823634004 16.961759713134892 chr6 171115067 336280124 1.9652280181732915 28.996967514224288 chr7 159138663 232126086 1.4586404185135073 21.91785771803945 chr8 146364022 162243104 1.1084903365117966 15.727646645437561 chr9 141213431 180216484 1.2761993156302534 18.255346051581707 chr10 135534747 200874451 1.482088213142863 19.64500882962347 chr11 135006516 227146835 1.6824879400635744 22.26505558202922 chr12 133851895 252826945 1.8888559254241413 23.551589967427944 chr13 115169878 92768232 0.8054904078304225 13.808075003907575 chr14 107349540 143191509 1.3338809742454416 18.346205719194014 chr15 102531392 164055288 1.600049358541821 21.787789291061017 chr16 90354753 136019353 1.505392339459995 19.89823800308149 chr17 81195210 176049209 2.1682216106097885 24.694921782677657 chr18 78077248 85177759 1.090942126956114 16.91701513050753 chr19 59128983 148429736 2.5102704032639966 26.918826632394914 chr20 63025520 111603383 1.7707649694917234 25.775646240674277 chr21 48129895 43309999 0.8998565029073926 17.2636806279458 chr22 51304566 73446218 1.4315727376000023 23.118939207810225 chrMT 16571 49255 2.9723613541729526 5.674294817158795 chrX 155270560 107839693 0.6945276232661234 11.435606735540775 chrY 59373566 8179825 0.13776880101828481 3.245545791462289