BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094071.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 496,818 number of mapped reads = 477,307 (96.07%) number of supplementary alignments = 15,655 (3.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 239,786 number of mapped paired reads (second in pair) = 237,521 number of mapped paired reads (both in pair) = 473,950 number of mapped paired reads (singletons) = 3,357 number of mapped bases = 63,203,332 bp number of sequenced bases = 61,658,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 459,610 duplication rate = 49.28% >>>>>>> Insert size mean insert size = 387,120.5719 std insert size = 5,688,845.9304 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 36.6924 >>>>>>> ACTG content number of A's = 16,955,767 bp (27.5%) number of C's = 14,061,117 bp (22.8%) number of T's = 15,999,794 bp (25.95%) number of G's = 14,640,953 bp (23.75%) number of N's = 710 bp (0%) GC percentage = 46.55% >>>>>>> Mismatches and indels general error rate = 0.0438 number of mismatches = 2,611,522 number of insertions = 45,120 mapped reads with insertion percentage = 9.26% number of deletions = 208,323 mapped reads with deletion percentage = 41.6% homopolymer indels = 27.15% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 6.0378X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 641342 0.0025730808510202267 1.3881416555045047 chr2 243199373 2325307 0.009561319880540976 3.362938591051828 chr3 198022430 1151574 0.005815371521296855 2.632586825763883 chr4 191154276 944791 0.004942557497379761 1.9811534941992575 chr5 180915260 461514 0.0025509954218345095 1.1149583669688066 chr6 171115067 1797170 0.01050269874832238 6.054405515025774 chr7 159138663 2128385 0.01337440543911067 5.264470361782375 chr8 146364022 728659 0.004978402410942219 1.3780781514953329 chr9 141213431 416954 0.002952651153982655 1.0912229412947738 chr10 135534747 1218685 0.008991679454715771 2.821951838876765 chr11 135006516 1511455 0.01119542259723227 3.025301442961158 chr12 133851895 1790364 0.013375709025262587 3.845391004740565 chr13 115169878 1425777 0.012379773468197996 4.103026641769046 chr14 107349540 277994 0.0025896151953701896 1.11014549505662 chr15 102531392 1115390 0.010878521965253334 4.078406510059823 chr16 90354753 555927 0.006152714511875208 1.9644269339361091 chr17 81195210 1057042 0.013018526585496853 3.8837547572985147 chr18 78077248 326186 0.004177734338177493 1.612226134033157 chr19 59128983 191858 0.003244737018392486 0.6985266205463659 chr20 63025520 327242 0.005192214201485366 1.6721412561446536 chr21 48129895 759136 0.0157726502416014 6.405472317247799 chr22 51304566 154893 0.003019088008657943 0.8051874562878034 chrMT 16571 2190677 132.19944481322793 599.1964413489281 chrX 155270560 38661763 0.24899609430145675 22.219650595019704 chrY 59373566 1043247 0.01757090015445594 4.460049085567957