BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927054.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 = 22,347,374 number of mapped reads = 21,735,158 (97.26%) number of supplementary alignments = 452,044 (2.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,896,152 number of mapped paired reads (second in pair) = 10,839,006 number of mapped paired reads (both in pair) = 21,371,884 number of mapped paired reads (singletons) = 363,274 number of mapped bases = 1,959,338,534 bp number of sequenced bases = 1,957,936,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,733,145 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 209,075.4297 std insert size = 4,446,390.5265 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.8883 >>>>>>> ACTG content number of A's = 561,575,553 bp (28.68%) number of C's = 375,031,111 bp (19.15%) number of T's = 575,338,361 bp (29.38%) number of G's = 445,740,613 bp (22.77%) number of N's = 250,662 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 20,480,536 number of insertions = 319,023 mapped reads with insertion percentage = 1.44% number of deletions = 963,476 mapped reads with deletion percentage = 4.32% homopolymer indels = 51.66% >>>>>>> Coverage mean coverageData = 0.6329X std coverageData = 2.5239X There is a 30.85% of reference with a coverageData >= 1X There is a 14.69% of reference with a coverageData >= 2X There is a 7.22% of reference with a coverageData >= 3X There is a 3.88% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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% 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 157567590 0.632165285558105 3.6790116867971214 chr2 243199373 174384762 0.7170444555381317 4.130285951858652 chr3 198022430 133139060 0.672343329995496 1.3493649255834372 chr4 191154276 121597449 0.6361220452112721 2.024906370155892 chr5 180915260 120740390 0.6673864327420473 1.336196666777068 chr6 171115067 115715596 0.6762443426445901 1.4052821299119413 chr7 159138663 102429288 0.6436480366810673 1.9853000764713435 chr8 146364022 101964782 0.6966519545356576 1.6694803533710771 chr9 141213431 84933794 0.6014569109931194 3.2454548039310045 chr10 135534747 95770817 0.7066144964287276 4.488751581487062 chr11 135006516 93386987 0.6917220721405772 2.468293313734465 chr12 133851895 88385272 0.6603214097193021 1.343787635223103 chr13 115169878 61825749 0.5368222149197727 1.2014641910773014 chr14 107349540 58118696 0.5413967866094256 1.2902278708286117 chr15 102531392 57210547 0.5579807889470573 1.2737072958282252 chr16 90354753 58757471 0.6502975111890351 3.5881146850178456 chr17 81195210 47702817 0.587507772933896 2.0298187902581333 chr18 78077248 52412368 0.671288619189037 3.328250916694391 chr19 59128983 29267774 0.49498186024948204 2.0851096233896125 chr20 63025520 43976896 0.6977633187318407 1.495350822958033 chr21 48129895 24204719 0.5029040474740284 1.6708238315905142 chr22 51304566 20956115 0.40846491129074164 1.1263339120493716 chrMT 16571 81562 4.92197211996862 2.6394159388395697 chrX 155270560 110603623 0.7123283576745005 1.5893734774678625 chrY 59373566 4204410 0.07081282603103206 1.7362080855668396