BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975324.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 = 4,335,530 number of mapped reads = 4,289,848 (98.95%) number of supplementary alignments = 23,418 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,144,227 number of mapped paired reads (second in pair) = 2,145,621 number of mapped paired reads (both in pair) = 4,273,656 number of mapped paired reads (singletons) = 16,192 number of mapped bases = 404,311,406 bp number of sequenced bases = 404,073,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,323 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 76,447.19 std insert size = 2,587,678.8282 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.7187 >>>>>>> ACTG content number of A's = 118,664,171 bp (29.37%) number of C's = 79,873,855 bp (19.77%) number of T's = 121,992,672 bp (30.19%) number of G's = 83,534,451 bp (20.67%) number of N's = 8,685 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 3,257,362 number of insertions = 67,857 mapped reads with insertion percentage = 1.55% number of deletions = 136,854 mapped reads with deletion percentage = 3.12% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.1306X std coverageData = 2.7553X There is a 8.76% of reference with a coverageData >= 1X There is a 2.52% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 37041997 0.14861345922183278 2.217829116985742 chr2 243199373 23203666 0.09541005683431593 1.611078722881993 chr3 198022430 16872464 0.08520481240433217 0.7733750657426032 chr4 191154276 25141061 0.13152235736541934 1.5738811170535276 chr5 180915260 22548233 0.12463422377968558 0.4616384341661318 chr6 171115067 26256879 0.15344574537086206 1.7695540057805053 chr7 159138663 19642679 0.1234312179686969 2.27453250204253 chr8 146364022 31245559 0.21347841206495405 0.8563820603467543 chr9 141213431 14890181 0.10544450973647117 1.9972432725084395 chr10 135534747 25966874 0.19158831646323138 11.178671267298467 chr11 135006516 17327148 0.128343049753243 1.7752754572284666 chr12 133851895 25599228 0.19125039656704151 0.5755209616310988 chr13 115169878 12058294 0.10470006749507887 0.4087981805810253 chr14 107349540 21158231 0.19709661541167292 0.6113670233054577 chr15 102531392 6522201 0.06361174731734842 0.3132185212265631 chr16 90354753 9192453 0.10173734855984831 2.0051633232835067 chr17 81195210 7292673 0.08981654213345837 1.433225143591691 chr18 78077248 19795940 0.25354300397473023 2.794844937127988 chr19 59128983 4100496 0.06934832618379383 1.1333543635993548 chr20 63025520 5110531 0.08108669313636761 0.516345008063085 chr21 48129895 5993327 0.1245239990654457 0.7046411279701986 chr22 51304566 3122834 0.06086853945904152 0.3213038755778014 chrMT 16571 93739 5.656810089916118 5.314584549281956 chrX 155270560 22854853 0.14719373073685058 0.897732492223245 chrY 59373566 1279865 0.021556141667488864 1.3853699653900495