BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927049.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 = 32,483,148 number of mapped reads = 31,760,492 (97.78%) number of supplementary alignments = 457,588 (1.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,943,211 number of mapped paired reads (second in pair) = 15,817,281 number of mapped paired reads (both in pair) = 31,333,476 number of mapped paired reads (singletons) = 427,016 number of mapped bases = 2,981,031,438 bp number of sequenced bases = 2,978,824,436 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,477,102 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 134,900.6915 std insert size = 3,586,715.502 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.3958 >>>>>>> ACTG content number of A's = 837,132,529 bp (28.1%) number of C's = 608,897,250 bp (20.44%) number of T's = 849,293,398 bp (28.51%) number of G's = 683,037,894 bp (22.93%) number of N's = 463,365 bp (0.02%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 30,446,708 number of insertions = 474,044 mapped reads with insertion percentage = 1.47% number of deletions = 1,553,846 mapped reads with deletion percentage = 4.77% homopolymer indels = 52.62% >>>>>>> Coverage mean coverageData = 0.963X std coverageData = 3.0402X There is a 34.03% of reference with a coverageData >= 1X There is a 20.16% of reference with a coverageData >= 2X There is a 12.52% of reference with a coverageData >= 3X There is a 8.24% of reference with a coverageData >= 4X There is a 5.59% of reference with a coverageData >= 5X There is a 3.89% of reference with a coverageData >= 6X There is a 2.76% of reference with a coverageData >= 7X There is a 1.99% of reference with a coverageData >= 8X There is a 1.46% of reference with a coverageData >= 9X There is a 1.08% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.61% of reference with a coverageData >= 12X There is a 0.46% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% 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 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 246136858 0.9875075015359741 4.037737085286406 chr2 243199373 264545987 1.0877741325426855 4.93618380438738 chr3 198022430 204026263 1.0303189542719984 2.105641339578727 chr4 191154276 171812541 0.8988161007708768 2.704745097854319 chr5 180915260 177549760 0.98139736802744 2.0564751153719256 chr6 171115067 164992643 0.9642204271819033 2.0369202807662106 chr7 159138663 138654450 0.8712807270474555 2.2845577050473445 chr8 146364022 152970182 1.0451351357371144 2.3856106483892403 chr9 141213431 127301220 0.9014809646541341 3.428572610951697 chr10 135534747 145056698 1.070254685316969 4.052340417861541 chr11 135006516 144648596 1.0714193676400035 3.2268470671989187 chr12 133851895 134898172 1.0078166767829473 2.1135980700765105 chr13 115169878 89114673 0.7737671911052992 1.8036963020568844 chr14 107349540 90981677 0.8475274044024781 1.983261334094668 chr15 102531392 91141915 0.888917171825776 2.0723061399318308 chr16 90354753 96889451 1.0723226812429003 4.376973028435462 chr17 81195210 81264125 1.0008487569648505 2.915807779397521 chr18 78077248 79406031 1.0170188247413638 3.4840846530416565 chr19 59128983 53288530 0.9012252079492049 2.7497931108082736 chr20 63025520 74127122 1.1761445522385219 2.483659491110789 chr21 48129895 38598889 0.8019732642259036 2.6320256698296607 chr22 51304566 40834287 0.7959191585403919 2.087674659520983 chrMT 16571 183472 11.071872548427976 9.133834658932585 chrX 155270560 168077315 1.0824802525346724 2.4747735881261193 chrY 59373566 4530581 0.07630636502446224 2.213789828433858