BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926907.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 26,148,160 number of mapped reads = 23,433,299 (89.62%) number of supplementary alignments = 367,333 (1.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,757,344 number of mapped paired reads (second in pair) = 11,675,955 number of mapped paired reads (both in pair) = 23,106,824 number of mapped paired reads (singletons) = 326,475 number of mapped bases = 2,181,719,320 bp number of sequenced bases = 2,180,095,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,473,245 duplication rate = 5.05% >>>>>>> Insert size mean insert size = 179,895.8429 std insert size = 4,176,074.1181 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.9524 >>>>>>> ACTG content number of A's = 613,193,360 bp (28.13%) number of C's = 442,035,491 bp (20.28%) number of T's = 618,774,235 bp (28.38%) number of G's = 505,886,855 bp (23.2%) number of N's = 205,254 bp (0.01%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 22,108,480 number of insertions = 344,960 mapped reads with insertion percentage = 1.45% number of deletions = 1,134,227 mapped reads with deletion percentage = 4.72% homopolymer indels = 52.61% >>>>>>> Coverage mean coverageData = 0.7048X std coverageData = 2.9762X There is a 30.95% of reference with a coverageData >= 1X There is a 15.91% of reference with a coverageData >= 2X There is a 8.65% of reference with a coverageData >= 3X There is a 5.08% of reference with a coverageData >= 4X There is a 3.1% of reference with a coverageData >= 5X There is a 1.95% of reference with a coverageData >= 6X There is a 1.26% of reference with a coverageData >= 7X There is a 0.83% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.01% 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 0.01% 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% 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 186560678 0.7484863116950871 2.329686460117131 chr2 243199373 184089757 0.756949965491893 3.289375779886776 chr3 198022430 136936267 0.6915189708559782 1.543742616635909 chr4 191154276 129302253 0.6764287763042246 1.6162519239582531 chr5 180915260 129514613 0.7158855090499275 1.499087086516133 chr6 171115067 109139325 0.6378124785469651 1.6072206113620673 chr7 159138663 113959372 0.7161011023449405 1.7086161910409348 chr8 146364022 112262351 0.7670078306539021 1.6908521900225295 chr9 141213431 97902190 0.693292339876651 2.7567406510039225 chr10 135534747 116196011 0.8573152905210352 10.641072979244843 chr11 135006516 106016681 0.7852708457419937 1.8651635758559704 chr12 133851895 101767548 0.7602996431242157 1.6087732083398143 chr13 115169878 64581382 0.5607488965126801 1.3255448065276612 chr14 107349540 62429220 0.581550885080644 1.3775638372410175 chr15 102531392 69414794 0.6770101589959883 1.5722601544713992 chr16 90354753 72912651 0.8069597733281392 2.9949249661521335 chr17 81195210 62331089 0.7676695337077151 1.7784083166975395 chr18 78077248 49965217 0.6399459289343805 2.5320150237925314 chr19 59128983 40738078 0.6889697054319368 1.7949674918578173 chr20 63025520 55824312 0.885741394914314 1.8642099260555596 chr21 48129895 27642166 0.5743242531486927 1.9148187609138003 chr22 51304566 25401285 0.4951076869064637 1.3296596534139193 chrMT 16571 15375 0.9278257196306801 1.205640228085926 chrX 155270560 123399501 0.794738558294631 1.6769270647167258 chrY 59373566 3417204 0.057554299500892366 1.3747865091785423