BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618590.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 51,015,138 number of mapped reads = 49,398,807 (96.83%) number of supplementary alignments = 185,901 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,936,899 number of mapped paired reads (second in pair) = 24,461,908 number of mapped paired reads (both in pair) = 48,672,934 number of mapped paired reads (singletons) = 725,873 number of mapped bases = 4,738,051,805 bp number of sequenced bases = 4,734,457,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,943,796 duplication rate = 24.07% >>>>>>> Insert size mean insert size = 69,689.8692 std insert size = 2,607,027.6402 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.8241 >>>>>>> ACTG content number of A's = 1,290,912,591 bp (27.27%) number of C's = 1,049,564,518 bp (22.17%) number of T's = 1,291,636,706 bp (27.28%) number of G's = 1,102,110,121 bp (23.28%) number of N's = 233,694 bp (0%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 60,715,983 number of insertions = 914,483 mapped reads with insertion percentage = 1.81% number of deletions = 2,517,712 mapped reads with deletion percentage = 4.96% homopolymer indels = 51.42% >>>>>>> Coverage mean coverageData = 1.5305X std coverageData = 7.1125X There is a 24.7% of reference with a coverageData >= 1X There is a 18.09% of reference with a coverageData >= 2X There is a 14.03% of reference with a coverageData >= 3X There is a 11.34% of reference with a coverageData >= 4X There is a 9.34% of reference with a coverageData >= 5X There is a 7.84% of reference with a coverageData >= 6X There is a 6.66% of reference with a coverageData >= 7X There is a 5.73% of reference with a coverageData >= 8X There is a 4.97% of reference with a coverageData >= 9X There is a 4.34% of reference with a coverageData >= 10X There is a 3.82% of reference with a coverageData >= 11X There is a 3.38% of reference with a coverageData >= 12X There is a 3% of reference with a coverageData >= 13X There is a 2.68% of reference with a coverageData >= 14X There is a 2.41% of reference with a coverageData >= 15X There is a 2.17% of reference with a coverageData >= 16X There is a 1.96% of reference with a coverageData >= 17X There is a 1.77% of reference with a coverageData >= 18X There is a 1.61% of reference with a coverageData >= 19X There is a 1.46% of reference with a coverageData >= 20X There is a 1.34% of reference with a coverageData >= 21X There is a 1.22% of reference with a coverageData >= 22X There is a 1.12% of reference with a coverageData >= 23X There is a 1.03% of reference with a coverageData >= 24X There is a 0.95% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.81% of reference with a coverageData >= 27X There is a 0.75% of reference with a coverageData >= 28X There is a 0.69% of reference with a coverageData >= 29X There is a 0.64% of reference with a coverageData >= 30X There is a 0.6% of reference with a coverageData >= 31X There is a 0.55% of reference with a coverageData >= 32X There is a 0.52% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.45% of reference with a coverageData >= 35X There is a 0.42% of reference with a coverageData >= 36X There is a 0.39% of reference with a coverageData >= 37X There is a 0.37% of reference with a coverageData >= 38X There is a 0.34% of reference with a coverageData >= 39X There is a 0.32% of reference with a coverageData >= 40X There is a 0.3% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 416355275 1.6704282353623505 7.684799360047204 chr2 243199373 397647757 1.635069005708333 9.698965755060067 chr3 198022430 301817447 1.5241578794887023 4.947816880034315 chr4 191154276 245023397 1.2818096572425093 7.838827741140025 chr5 180915260 266519240 1.473171693753197 5.075321293350912 chr6 171115067 249152266 1.4560510092311159 5.567233387540956 chr7 159138663 227411301 1.4290135201148448 5.465601862561015 chr8 146364022 239059063 1.6333184872440851 5.757340791435547 chr9 141213431 205902223 1.4580923467541838 8.74011270441984 chr10 135534747 236145466 1.7423241731509633 8.13401118606648 chr11 135006516 241487883 1.7887127981289437 6.115730732123641 chr12 133851895 208301075 1.556205648041068 5.586033991811212 chr13 115169878 118595977 1.0297482211451157 3.882031902730996 chr14 107349540 141616172 1.3192061372596473 4.991401898029711 chr15 102531392 150746858 1.470250769637459 5.222261859915661 chr16 90354753 169612739 1.8771866821438823 10.467269591413684 chr17 81195210 157327543 1.93764561973545 7.61918785589334 chr18 78077248 119596610 1.5317728667895671 10.5666032817073 chr19 59128983 94760872 1.6026129182705544 6.077430941833305 chr20 63025520 135565697 2.150965148720709 6.818466555714984 chr21 48129895 61893784 1.2859738006908181 14.334979865320243 chr22 51304566 86593688 1.6878358935927846 6.519068459503622 chrMT 16571 41820 2.52368595739545 7.639593769798315 chrX 155270560 257503085 1.6584153815121168 5.274151426062186 chrY 59373566 9374567 0.15789125753369773 5.159393923837415