BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053624.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 14,232,679 number of mapped reads = 10,208,474 (71.73%) number of supplementary alignments = 302 (0%) number of secondary alignments = 0 number of mapped bases = 482,232,967 bp number of sequenced bases = 482,131,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,770,419 duplication rate = 18.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7239 >>>>>>> ACTG content number of A's = 143,889,964 bp (29.84%) number of C's = 90,659,922 bp (18.8%) number of T's = 147,816,953 bp (30.66%) number of G's = 99,616,972 bp (20.66%) number of N's = 147,921 bp (0.03%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 3,019,073 number of insertions = 21,706 mapped reads with insertion percentage = 0.21% number of deletions = 68,678 mapped reads with deletion percentage = 0.67% homopolymer indels = 48.17% >>>>>>> Coverage mean coverageData = 0.1558X std coverageData = 1.152X There is a 5.74% of reference with a coverageData >= 1X There is a 2.67% of reference with a coverageData >= 2X There is a 1.67% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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% 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 37780079 0.15157466347897283 1.214968505634453 chr2 243199373 40862808 0.1680218476550102 1.2452426849267408 chr3 198022430 33457255 0.16895689543856218 1.1414610480746454 chr4 191154276 32546143 0.1702611298111898 1.2030616549164714 chr5 180915260 30427611 0.16818708935885232 1.1302125951218065 chr6 171115067 28861975 0.16866998041732936 1.198016498257073 chr7 159138663 26346181 0.1655548721054669 1.2202059333318724 chr8 146364022 24649881 0.16841489228821546 1.225928234754307 chr9 141213431 19907453 0.14097421795523118 1.0621442822328586 chr10 135534747 22078586 0.162899820811264 1.204701781489937 chr11 135006516 21946690 0.16256022783374396 1.1705817839199708 chr12 133851895 22132512 0.16535075577376024 1.1222636691580754 chr13 115169878 16157590 0.14029354098994531 1.0511213398917225 chr14 107349540 14849253 0.13832619124404258 1.1295569978892743 chr15 102531392 13689995 0.1335200345275718 0.9855240568795584 chr16 90354753 12949804 0.14332177965225582 1.093808687371893 chr17 81195210 11821075 0.1455883296563923 1.0089062056209104 chr18 78077248 12921593 0.16549754673730305 1.2910961256699314 chr19 59128983 7989729 0.1351237344975137 1.1395860545813352 chr20 63025520 9534243 0.15127591172591673 1.0628988033268383 chr21 48129895 6130827 0.12738085133990007 1.0190817674069024 chr22 51304566 4841725 0.09437220461040446 0.8055387572292518 chrMT 16571 29352 1.7712871884617705 4.341098878234096 chrX 155270560 29096780 0.18739405589829777 1.2873913747862535 chrY 59373566 1223827 0.020612320977992125 0.40471220870632657