BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124969.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,239,730 number of mapped reads = 4,961,762 (94.69%) number of supplementary alignments = 16,252 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,524,091 number of mapped paired reads (second in pair) = 2,437,671 number of mapped paired reads (both in pair) = 4,847,574 number of mapped paired reads (singletons) = 114,188 number of mapped bases = 304,488,803 bp number of sequenced bases = 304,349,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,113 duplication rate = 6.04% >>>>>>> Insert size mean insert size = 78,816.4683 std insert size = 2,700,703.8561 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 51.5003 >>>>>>> ACTG content number of A's = 83,860,662 bp (27.55%) number of C's = 54,522,561 bp (17.91%) number of T's = 90,558,604 bp (29.75%) number of G's = 75,407,682 bp (24.78%) number of N's = 3 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 2,186,489 number of insertions = 38,165 mapped reads with insertion percentage = 0.76% number of deletions = 85,139 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0984X std coverageData = 1.1792X There is a 7.24% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% 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 0.02% 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 24646219 0.09888127420151945 0.6995483446503584 chr2 243199373 27262248 0.11209834821408031 1.4032980597408984 chr3 198022430 20208530 0.10205172212056987 0.4718151251165466 chr4 191154276 20128262 0.10529851814562599 0.8926162469041267 chr5 180915260 18359059 0.10147877520116325 0.42649404803236035 chr6 171115067 17871974 0.10444418667118308 0.5204923706535972 chr7 159138663 16161424 0.10155561002796662 0.6887626272114241 chr8 146364022 15462930 0.10564706946902566 0.4711619918012493 chr9 141213431 12808996 0.09070664107014013 0.7756290997273999 chr10 135534747 18042312 0.13311945755135396 4.241062898948297 chr11 135006516 14057749 0.10412644823750582 0.5417106576856257 chr12 133851895 13384127 0.09999206212209398 0.4062877418702584 chr13 115169878 9348587 0.081172153364615 0.35625503735654407 chr14 107349540 9175263 0.08547091119347135 0.44504599789484856 chr15 102531392 8786565 0.08569633971223174 0.3758764402186438 chr16 90354753 10598939 0.1173036132365942 1.7571127140889529 chr17 81195210 7581190 0.09336991677218398 0.6998610926518535 chr18 78077248 8255084 0.10572969989925875 1.115290697026234 chr19 59128983 4706548 0.07959798665909745 0.6103094689635888 chr20 63025520 6486039 0.10291131275077144 0.5730588143702078 chr21 48129895 3959971 0.08227674296816978 0.5363543056632418 chr22 51304566 3296723 0.06425788691010464 0.3867077894774296 chrMT 16571 152667 9.21290205781184 6.797164858617523 chrX 155270560 9375987 0.060384834059978916 0.40544046618171037 chrY 59373566 4371410 0.0736255255411137 1.726552419697267