BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975284.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,321,822 number of mapped reads = 5,270,559 (99.04%) number of supplementary alignments = 35,247 (0.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,634,505 number of mapped paired reads (second in pair) = 2,636,054 number of mapped paired reads (both in pair) = 5,251,286 number of mapped paired reads (singletons) = 19,273 number of mapped bases = 495,156,640 bp number of sequenced bases = 494,851,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,674 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 89,767.0094 std insert size = 2,858,809.5629 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 52.8812 >>>>>>> ACTG content number of A's = 144,326,877 bp (29.17%) number of C's = 100,097,017 bp (20.23%) number of T's = 144,295,826 bp (29.16%) number of G's = 106,117,664 bp (21.44%) number of N's = 14,025 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 4,254,382 number of insertions = 93,647 mapped reads with insertion percentage = 1.74% number of deletions = 173,061 mapped reads with deletion percentage = 3.21% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.16X std coverageData = 1.8384X There is a 10.24% of reference with a coverageData >= 1X There is a 3.31% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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% 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 45861485 0.18399747537640038 1.6997377533089 chr2 243199373 41588449 0.17100557656454154 1.7248761852697347 chr3 198022430 34127876 0.17234348654341833 0.6308952717442085 chr4 191154276 21635368 0.11318275715684226 1.5768721999587465 chr5 180915260 30557653 0.1689058899730183 0.5549221323289416 chr6 171115067 39651798 0.23172592978033899 1.3551252992318659 chr7 159138663 27967314 0.17574179318070557 1.588648289056344 chr8 146364022 25176816 0.1720150598211902 0.7386463718803778 chr9 141213431 21195917 0.1500984492048777 2.1581033627582316 chr10 135534747 27798768 0.20510436338513252 5.731237396819 chr11 135006516 18368728 0.1360580847816264 1.7086855120865425 chr12 133851895 21408583 0.15994232281881404 0.5385360555084825 chr13 115169878 16194898 0.14061747985875264 0.505502396462695 chr14 107349540 14550070 0.13553919280883736 0.5351350499014983 chr15 102531392 14293458 0.13940567587339495 0.5033090093021981 chr16 90354753 17538394 0.1941059370722866 2.742314235642623 chr17 81195210 10435215 0.128520081418596 1.2640791408837082 chr18 78077248 13856581 0.17747271266528247 2.1658759104733543 chr19 59128983 6578128 0.11125048438597362 1.0530509861910557 chr20 63025520 11475128 0.18207113562886906 0.6756674283635562 chr21 48129895 6195688 0.12872847530625198 0.8014338962398286 chr22 51304566 5311928 0.10353713936494463 0.45367894060725744 chrMT 16571 104063 6.279826202401786 5.382873590092761 chrX 155270560 15219305 0.09801796940772288 0.7297678844532802 chrY 59373566 8065029 0.13583534800655228 3.1417994306580885