BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472792.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 = 8,038,992 number of mapped reads = 7,976,334 (99.22%) number of supplementary alignments = 26,561 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,999,003 number of mapped paired reads (second in pair) = 3,977,331 number of mapped paired reads (both in pair) = 7,938,164 number of mapped paired reads (singletons) = 38,170 number of mapped bases = 782,276,659 bp number of sequenced bases = 782,169,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,405,389 duplication rate = 43.22% >>>>>>> Insert size mean insert size = 23,601.7329 std insert size = 1,543,694.9825 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 55.2563 >>>>>>> ACTG content number of A's = 213,002,221 bp (27.23%) number of C's = 179,442,955 bp (22.94%) number of T's = 211,394,206 bp (27.03%) number of G's = 178,177,807 bp (22.78%) number of N's = 152,523 bp (0.02%) GC percentage = 45.72% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 4,456,841 number of insertions = 41,334 mapped reads with insertion percentage = 0.51% number of deletions = 42,226 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.2527X std coverageData = 9.6139X There is a 2.41% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 95929196 0.384870439299728 15.026052241944871 chr2 243199373 62685732 0.25775449676015405 10.431037984812118 chr3 198022430 92490338 0.4670700081803864 11.132301176450481 chr4 191154276 28557440 0.14939472240736063 6.610545590542503 chr5 180915260 34090817 0.18843527627243828 6.256034516974812 chr6 171115067 56418001 0.32970796779689776 11.020839676880579 chr7 159138663 31968350 0.2008836155673873 6.5358176483589485 chr8 146364022 34744912 0.23738697205246245 8.046955543653704 chr9 141213431 41857616 0.2964138446575949 7.899663336943016 chr10 135534747 18074733 0.13335866558263468 4.27138808593569 chr11 135006516 27296307 0.20218510786546037 6.452040370358801 chr12 133851895 42607771 0.31832026733726854 12.334487357442633 chr13 115169878 15719983 0.13649387559479745 4.841283089880739 chr14 107349540 20166649 0.18785966851837466 9.759952978718541 chr15 102531392 14945897 0.14576898556102702 4.640732244667113 chr16 90354753 31896408 0.35301306174784186 13.699344986735694 chr17 81195210 31468597 0.3875671606736407 11.50079517162333 chr18 78077248 10438127 0.1336897401916625 5.498602286488469 chr19 59128983 11130109 0.18823440612871695 4.715050588252042 chr20 63025520 27944328 0.44338115734705563 21.332719573545532 chr21 48129895 4388825 0.09118708860677963 4.5212535508504645 chr22 51304566 8164859 0.15914488000931534 5.509055414148552 chrMT 16571 1207 0.07283809064027517 0.28332769393096574 chrX 155270560 38326580 0.24683739145398845 8.525291684606644 chrY 59373566 963877 0.016234109974125523 0.7622717158661237