BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472522.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,207,746 number of mapped reads = 14,054,167 (98.92%) number of supplementary alignments = 66,829 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,050,782 number of mapped paired reads (second in pair) = 7,003,385 number of mapped paired reads (both in pair) = 13,969,904 number of mapped paired reads (singletons) = 84,263 number of mapped bases = 1,384,534,882 bp number of sequenced bases = 1,384,359,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,163,351 duplication rate = 42.66% >>>>>>> Insert size mean insert size = 25,923.2985 std insert size = 1,576,785.3252 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 54.7953 >>>>>>> ACTG content number of A's = 395,573,057 bp (28.57%) number of C's = 298,414,339 bp (21.56%) number of T's = 393,466,021 bp (28.42%) number of G's = 296,692,340 bp (21.43%) number of N's = 213,282 bp (0.02%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,379,249 number of insertions = 75,439 mapped reads with insertion percentage = 0.53% number of deletions = 74,983 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.4472X std coverageData = 23.1186X There is a 4.57% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.17% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 122163797 0.49012434356181606 22.65302835339311 chr2 243199373 116983430 0.48101863321826904 35.40482243365074 chr3 198022430 165111392 0.8338014638038731 25.45558552518066 chr4 191154276 51671370 0.27031239416271285 8.794151462729745 chr5 180915260 92161650 0.5094188848414446 28.663061207980878 chr6 171115067 78163948 0.4567917330155386 14.132899063327757 chr7 159138663 51297252 0.32234311281099554 10.101923561638872 chr8 146364022 56499686 0.3860216822956669 15.538394972711663 chr9 141213431 131336860 0.9300592661047943 50.34601899501171 chr10 135534747 45397104 0.33494808530538667 21.660500925142344 chr11 135006516 47871609 0.3545873963594468 17.06370398460165 chr12 133851895 49304557 0.36835157993093787 14.798012294865162 chr13 115169878 31742751 0.27561678063078265 11.960825464777944 chr14 107349540 48348049 0.4503796569598715 20.804269130619247 chr15 102531392 36262860 0.35367568207793376 15.80517678256288 chr16 90354753 42468146 0.47001562828687055 21.56395620261347 chr17 81195210 60141364 0.7407008861729651 33.91186235675902 chr18 78077248 26787882 0.3430945978013979 13.402454265478713 chr19 59128983 15078729 0.25501417807236765 9.560782061530192 chr20 63025520 20740761 0.32908512297875525 13.655608517200507 chr21 48129895 4638663 0.09637799957801695 6.707552758913509 chr22 51304566 6704624 0.13068279341842595 4.705971408408318 chrMT 16571 3116 0.18803934584515117 0.4987504389802468 chrX 155270560 82345638 0.5303364527055225 24.809565682472886 chrY 59373566 1309644 0.022057694833421324 0.9446959796064337