BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038471.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 20,299,416 number of mapped reads = 19,704,497 (97.07%) number of supplementary alignments = 211,020 (1.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,911,080 number of mapped paired reads (second in pair) = 9,793,417 number of mapped paired reads (both in pair) = 19,564,164 number of mapped paired reads (singletons) = 140,333 number of mapped bases = 2,902,249,940 bp number of sequenced bases = 2,901,253,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,183,760 duplication rate = 8.67% >>>>>>> Insert size mean insert size = 109,083.2812 std insert size = 3,310,403.2446 median insert size = 282 >>>>>>> Mapping quality mean mapping quality = 54.3451 >>>>>>> ACTG content number of A's = 832,493,417 bp (28.69%) number of C's = 620,812,162 bp (21.4%) number of T's = 826,704,947 bp (28.49%) number of G's = 620,974,525 bp (21.4%) number of N's = 267,991 bp (0.01%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 25,144,120 number of insertions = 337,382 mapped reads with insertion percentage = 1.62% number of deletions = 366,471 mapped reads with deletion percentage = 1.78% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 0.9375X std coverageData = 9.1458X There is a 49.31% of reference with a coverageData >= 1X There is a 23.92% of reference with a coverageData >= 2X There is a 10% of reference with a coverageData >= 3X There is a 4.25% of reference with a coverageData >= 4X There is a 1.71% of reference with a coverageData >= 5X There is a 0.73% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 250138558 1.0035624264302234 23.158827491189143 chr2 243199373 245398108 1.0090408744598203 7.379211253654791 chr3 198022430 194884856 0.9841554615807916 1.3455608598108921 chr4 191154276 154092622 0.8061165317588815 5.672371600419218 chr5 180915260 181576986 1.0036576571815998 1.315935931025341 chr6 171115067 164513760 0.9614218249991978 4.181960143887322 chr7 159138663 149581731 0.9399458822900881 7.322549432072899 chr8 146364022 159053225 1.0866961895868097 5.954644391201354 chr9 141213431 123400868 0.8738607023860216 10.027868544233401 chr10 135534747 155022871 1.143786921297754 19.257388482632795 chr11 135006516 133847965 0.9914185549384891 4.061308756954999 chr12 133851895 125588280 0.9382629958283369 1.5234531963427433 chr13 115169878 92444192 0.8026768249246561 1.1751399735434842 chr14 107349540 91131985 0.8489275780781175 1.2600136275461618 chr15 102531392 83237301 0.8118225977074416 1.20135426055099 chr16 90354753 91721954 1.015131478473523 5.241434640557725 chr17 81195210 85765562 1.0562884436163167 5.150521674604302 chr18 78077248 92507301 1.1848176436751459 8.436888527808211 chr19 59128983 60487855 1.0229814877756311 9.471503738244099 chr20 63025520 73013126 1.1584692359539437 2.2701458645578914 chr21 48129895 36452803 0.7573838048057242 3.092630450216229 chr22 51304566 31195918 0.6080534430405278 1.0754507327188534 chrMT 16571 5585639 337.0731398225816 37.986951660620285 chrX 155270560 114765294 0.7391310625787657 1.9475370781853854 chrY 59373566 6841180 0.11522265649329536 5.935642026483511