BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975229.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/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 = 3,711,736 number of mapped reads = 3,666,447 (98.78%) number of supplementary alignments = 14,727 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,832,621 number of mapped paired reads (second in pair) = 1,833,826 number of mapped paired reads (both in pair) = 3,649,772 number of mapped paired reads (singletons) = 16,675 number of mapped bases = 332,222,572 bp number of sequenced bases = 332,043,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,923 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 50,979.8552 std insert size = 2,100,739.1601 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.6488 >>>>>>> ACTG content number of A's = 97,662,168 bp (29.41%) number of C's = 63,245,547 bp (19.05%) number of T's = 101,102,441 bp (30.45%) number of G's = 70,028,735 bp (21.09%) number of N's = 4,625 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 2,731,571 number of insertions = 46,940 mapped reads with insertion percentage = 1.25% number of deletions = 102,271 mapped reads with deletion percentage = 2.73% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.1073X std coverageData = 1.35X There is a 7.42% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% 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% 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 25466910 0.10217390792378407 1.196313289671814 chr2 243199373 30639861 0.1259865953684017 1.5260329854520653 chr3 198022430 23584362 0.11909944747168288 0.48933830300646053 chr4 191154276 23488080 0.12287499129760508 0.9390399417123368 chr5 180915260 21229016 0.1173423181659745 0.4441703661480726 chr6 171115067 19806083 0.1157471597752406 0.6516189760447457 chr7 159138663 17907543 0.11252792164026161 1.148121769384202 chr8 146364022 17418164 0.11900577588664515 0.5692746395622806 chr9 141213431 14101931 0.09986253361410077 1.6148740584098906 chr10 135534747 18717949 0.13810443015029938 4.113803982369065 chr11 135006516 15220632 0.1127399806391567 0.9344527692199933 chr12 133851895 14661942 0.1095385463164343 0.42570195857337134 chr13 115169878 10745617 0.09330232163656542 0.38578405641758495 chr14 107349540 9993775 0.09309564810431419 0.428289203916221 chr15 102531392 8889837 0.08670356294392258 0.3752616521425791 chr16 90354753 11494847 0.12721906284221707 2.698109478397337 chr17 81195210 6886085 0.08480900535881365 1.2049533322362005 chr18 78077248 9577963 0.1226729072213201 1.7939604836692151 chr19 59128983 3471230 0.0587060663634279 0.6868078313369582 chr20 63025520 6269919 0.09948222561273593 0.45131570955465655 chr21 48129895 4291208 0.08915888970877664 0.5297232723700763 chr22 51304566 2636479 0.05138877892466725 0.3153053613310822 chrMT 16571 52075 3.14253816909058 2.645215601922311 chrX 155270560 11480851 0.07394093896486237 0.5129347525599247 chrY 59373566 4190213 0.07057371288765105 1.608023470678907