BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472601.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 = 8,564,728 number of mapped reads = 8,026,227 (93.71%) number of supplementary alignments = 264,761 (3.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,047,463 number of mapped paired reads (second in pair) = 3,978,764 number of mapped paired reads (both in pair) = 7,854,800 number of mapped paired reads (singletons) = 171,427 number of mapped bases = 653,972,520 bp number of sequenced bases = 653,701,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,254,399 duplication rate = 14% >>>>>>> Insert size mean insert size = 246,904.8921 std insert size = 4,787,382.9692 median insert size = 127 >>>>>>> Mapping quality mean mapping quality = 50.5957 >>>>>>> ACTG content number of A's = 171,203,864 bp (26.19%) number of C's = 130,436,744 bp (19.95%) number of T's = 194,650,168 bp (29.78%) number of G's = 156,995,754 bp (24.02%) number of N's = 414,827 bp (0.06%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 7,464,137 number of insertions = 59,810 mapped reads with insertion percentage = 0.73% number of deletions = 145,019 mapped reads with deletion percentage = 1.77% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.2113X std coverageData = 1.6968X There is a 11.67% of reference with a coverageData >= 1X There is a 5.31% of reference with a coverageData >= 2X There is a 1.84% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 40289234 0.1616414588591938 2.109283069887516 chr2 243199373 62297940 0.2561599531755372 2.603455398403631 chr3 198022430 32881046 0.16604707860619627 0.6071885547125376 chr4 191154276 31540669 0.16500111668964182 0.8844847760232338 chr5 180915260 29659775 0.16394291448935816 0.6230304563641725 chr6 171115067 41560150 0.24287837844226773 1.1265531985262947 chr7 159138663 52518402 0.33001660947723305 3.4460558073612453 chr8 146364022 30802489 0.21045123370550722 1.5571164837819707 chr9 141213431 21332194 0.1510634919705336 1.874992838828751 chr10 135534747 34739161 0.25631184451910327 1.7490950731178425 chr11 135006516 33264565 0.2463922926505266 1.9514198416580453 chr12 133851895 31586060 0.23597768264692853 0.7664793233370284 chr13 115169878 36325771 0.3154103454029881 0.9117559490995455 chr14 107349540 14986205 0.13960194892311603 1.4764305274384786 chr15 102531392 18211026 0.17761414962551175 0.6510055054468665 chr16 90354753 22297166 0.24677358146283682 1.0521585610298494 chr17 81195210 18176112 0.22385694919687996 1.2174973726799925 chr18 78077248 13829576 0.17712683725737874 3.2492420468289693 chr19 59128983 10153963 0.17172564933173295 1.5521071661083503 chr20 63025520 20919880 0.3319271304703238 1.0182738858209786 chr21 48129895 9541379 0.19824225670968115 0.8969737225318875 chr22 51304566 5843121 0.11389085719972761 0.5163438949577255 chrMT 16571 57682 3.4809003681129687 3.4166380575422597 chrX 155270560 39749663 0.2560025738298361 1.082122066326643 chrY 59373566 1409291 0.02373600063031417 0.6440338973682427