BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617495.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,752,029 (96.1%) number of supplementary alignments = 138,256 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,402,744 number of mapped paired reads (second in pair) = 15,349,285 number of mapped paired reads (both in pair) = 30,330,272 number of mapped paired reads (singletons) = 421,757 number of mapped bases = 3,010,213,699 bp number of sequenced bases = 3,008,420,316 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,404,063 duplication rate = 10.05% >>>>>>> Insert size mean insert size = 29,812.932 std insert size = 1,595,436.9216 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.8178 >>>>>>> ACTG content number of A's = 887,153,804 bp (29.49%) number of C's = 608,474,750 bp (20.23%) number of T's = 887,146,771 bp (29.49%) number of G's = 623,745,442 bp (20.73%) number of N's = 1,899,549 bp (0.06%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 35,031,932 number of insertions = 446,748 mapped reads with insertion percentage = 1.42% number of deletions = 1,050,498 mapped reads with deletion percentage = 3.34% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.9724X std coverageData = 9.85X There is a 38.51% of reference with a coverageData >= 1X There is a 20.85% of reference with a coverageData >= 2X There is a 11.82% of reference with a coverageData >= 3X There is a 7.05% of reference with a coverageData >= 4X There is a 4.36% of reference with a coverageData >= 5X There is a 2.81% of reference with a coverageData >= 6X There is a 1.86% of reference with a coverageData >= 7X There is a 1.27% of reference with a coverageData >= 8X There is a 0.9% of reference with a coverageData >= 9X There is a 0.65% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% 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 193923879 0.7780276663784119 9.580220072794681 chr2 243199373 311104841 1.279217282357056 11.65557361861668 chr3 198022430 248526570 1.2550425222031665 2.2625350077799737 chr4 191154276 155491136 0.8134326851260183 6.310259290438532 chr5 180915260 193420639 1.0691228534287267 2.1012534405392884 chr6 171115067 141762543 0.8284632410540447 5.460841404268395 chr7 159138663 232178165 1.4589676739963562 13.18575276104145 chr8 146364022 133729285 0.9136759373830271 3.838027369574282 chr9 141213431 124775702 0.8835965610098376 18.807402152938693 chr10 135534747 127529732 0.9409375442298941 18.973446532416578 chr11 135006516 169780350 1.257571523436691 12.874342398963767 chr12 133851895 131599627 0.9831734320982157 2.0077454365365663 chr13 115169878 127766379 1.1093732251761177 2.136514128413693 chr14 107349540 87582289 0.8158608690824386 2.230233764691533 chr15 102531392 67831796 0.6615710045173288 1.4571652667820918 chr16 90354753 81017449 0.8966595149676299 14.906640281582098 chr17 81195210 84231563 1.03739571583102 13.882196801757447 chr18 78077248 53821596 0.6893377696918825 17.25037799665624 chr19 59128983 35782313 0.6051569160254286 5.989935826355369 chr20 63025520 88701854 1.4073958294989077 2.812777118476176 chr21 48129895 43228212 0.8981572056203322 3.8725863847478954 chr22 51304566 22585852 0.4402308363742907 1.2528817134497399 chrMT 16571 2107998 127.21006577756322 93.5589373730165 chrX 155270560 141292243 0.9099744536246923 4.114038320652296 chrY 59373566 10441686 0.17586422213548702 13.932820229632107