BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927003.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 = 11,462,630 number of mapped reads = 11,189,064 (97.61%) number of supplementary alignments = 312,733 (2.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,600,980 number of mapped paired reads (second in pair) = 5,588,084 number of mapped paired reads (both in pair) = 11,020,302 number of mapped paired reads (singletons) = 168,762 number of mapped bases = 1,022,210,114 bp number of sequenced bases = 1,021,425,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 640,169 duplication rate = 4.61% >>>>>>> Insert size mean insert size = 291,047.0726 std insert size = 5,237,572.187 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 52.7083 >>>>>>> ACTG content number of A's = 293,873,858 bp (28.77%) number of C's = 197,297,987 bp (19.32%) number of T's = 298,785,647 bp (29.25%) number of G's = 231,275,281 bp (22.64%) number of N's = 193,108 bp (0.02%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 9,749,872 number of insertions = 176,689 mapped reads with insertion percentage = 1.55% number of deletions = 534,744 mapped reads with deletion percentage = 4.66% homopolymer indels = 52.08% >>>>>>> Coverage mean coverageData = 0.3302X std coverageData = 1.4211X There is a 19.87% of reference with a coverageData >= 1X There is a 7.47% of reference with a coverageData >= 2X There is a 2.83% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 84324201 0.3383108963247077 1.9162288348964238 chr2 243199373 89531449 0.36814013085469594 2.4128439336943566 chr3 198022430 67818233 0.3424775314594412 0.8341486845795211 chr4 191154276 64101984 0.3353416169460944 1.1602749875046663 chr5 180915260 62872306 0.3475235090727007 0.8397322134313402 chr6 171115067 60009611 0.35069741111692987 0.9981326001538855 chr7 159138663 53734091 0.33765579015829733 1.0885372247118579 chr8 146364022 53116559 0.36290721089913747 0.9967488602811275 chr9 141213431 42627270 0.30186413358938924 1.6596314394310134 chr10 135534747 47020373 0.34692485905477805 2.5924208963091986 chr11 135006516 48539187 0.3595321799134495 1.122201350719597 chr12 133851895 46172387 0.34495131353949077 0.855913396792745 chr13 115169878 31787870 0.27600854105272216 0.7452204398662188 chr14 107349540 30956725 0.28837314999207264 0.7818498573103456 chr15 102531392 29145859 0.28426278461137056 0.7710588229512167 chr16 90354753 31594294 0.3496694191616018 1.833945736615554 chr17 81195210 25978497 0.3199511030268904 1.0417682676287774 chr18 78077248 27066846 0.34666752086344027 1.6955027044784032 chr19 59128983 16342500 0.2763873006237905 1.278232496552794 chr20 63025520 23552749 0.3737017798504479 0.9239095190531813 chr21 48129895 13252815 0.2753551612776217 1.1310461663940505 chr22 51304566 11358632 0.2213961229103858 0.69698207379842 chrMT 16571 219957 13.273610524410113 12.250495681252026 chrX 155270560 59061848 0.3803802085855812 0.9865129631449239 chrY 59373566 2023871 0.03408707167765534 1.4021086339627833