BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438266.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 741,482,424 number of mapped reads = 739,174,889 (99.69%) number of supplementary alignments = 12,399,987 (1.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 369,804,743 number of mapped paired reads (second in pair) = 369,370,146 number of mapped paired reads (both in pair) = 737,537,242 number of mapped paired reads (singletons) = 1,637,647 number of mapped bases = 106,607,255,835 bp number of sequenced bases = 106,577,261,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 322,257,316 duplication rate = 40.88% >>>>>>> Insert size mean insert size = 43,834.687 std insert size = 2,049,933.2123 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 55.0738 >>>>>>> ACTG content number of A's = 32,237,633,285 bp (30.25%) number of C's = 21,297,944,294 bp (19.98%) number of T's = 30,756,354,162 bp (28.86%) number of G's = 22,284,670,323 bp (20.91%) number of N's = 659,769 bp (0%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 547,772,792 number of insertions = 13,568,966 mapped reads with insertion percentage = 1.81% number of deletions = 12,107,129 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.47% >>>>>>> Coverage mean coverageData = 34.4373X std coverageData = 109.1335X There is a 91.59% of reference with a coverageData >= 1X There is a 91.04% of reference with a coverageData >= 2X There is a 90.41% of reference with a coverageData >= 3X There is a 89.72% of reference with a coverageData >= 4X There is a 88.94% of reference with a coverageData >= 5X There is a 88.07% of reference with a coverageData >= 6X There is a 87.11% of reference with a coverageData >= 7X There is a 86.04% of reference with a coverageData >= 8X There is a 84.89% of reference with a coverageData >= 9X There is a 83.64% of reference with a coverageData >= 10X There is a 82.3% of reference with a coverageData >= 11X There is a 80.89% of reference with a coverageData >= 12X There is a 79.4% of reference with a coverageData >= 13X There is a 77.84% of reference with a coverageData >= 14X There is a 76.21% of reference with a coverageData >= 15X There is a 74.54% of reference with a coverageData >= 16X There is a 72.82% of reference with a coverageData >= 17X There is a 71.06% of reference with a coverageData >= 18X There is a 69.26% of reference with a coverageData >= 19X There is a 67.45% of reference with a coverageData >= 20X There is a 65.62% of reference with a coverageData >= 21X There is a 63.77% of reference with a coverageData >= 22X There is a 61.92% of reference with a coverageData >= 23X There is a 60.08% of reference with a coverageData >= 24X There is a 58.24% of reference with a coverageData >= 25X There is a 56.41% of reference with a coverageData >= 26X There is a 54.6% of reference with a coverageData >= 27X There is a 52.82% of reference with a coverageData >= 28X There is a 51.05% of reference with a coverageData >= 29X There is a 49.32% of reference with a coverageData >= 30X There is a 47.61% of reference with a coverageData >= 31X There is a 45.94% of reference with a coverageData >= 32X There is a 44.3% of reference with a coverageData >= 33X There is a 42.7% of reference with a coverageData >= 34X There is a 41.14% of reference with a coverageData >= 35X There is a 39.61% of reference with a coverageData >= 36X There is a 38.13% of reference with a coverageData >= 37X There is a 36.69% of reference with a coverageData >= 38X There is a 35.29% of reference with a coverageData >= 39X There is a 33.93% of reference with a coverageData >= 40X There is a 32.61% of reference with a coverageData >= 41X There is a 31.34% of reference with a coverageData >= 42X There is a 30.11% of reference with a coverageData >= 43X There is a 28.91% of reference with a coverageData >= 44X There is a 27.76% of reference with a coverageData >= 45X There is a 26.65% of reference with a coverageData >= 46X There is a 25.57% of reference with a coverageData >= 47X There is a 24.54% of reference with a coverageData >= 48X There is a 23.54% of reference with a coverageData >= 49X There is a 22.58% of reference with a coverageData >= 50X There is a 21.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8664544994 34.76238076855183 33.74874686115913 chr2 243199373 9442568621 38.826451337109326 140.29091441899155 chr3 198022430 7719677819 38.98385561171025 39.02622802059229 chr4 191154276 7264428782 38.00296249716119 26.40385137116546 chr5 180915260 6948641645 38.408267190948955 27.15131046661232 chr6 171115067 6363972328 37.19118625597125 28.34386675070146 chr7 159138663 5826470866 36.6125412653492 27.25173769767462 chr8 146364022 5428873705 37.09158597049212 27.31449690758953 chr9 141213431 4646225774 32.902152019803275 34.63768608949849 chr10 135534747 5083043626 37.503619835583564 39.47179988202656 chr11 135006516 4885337297 36.18593710691712 27.80881309140733 chr12 133851895 4939307245 36.901287389319364 26.63778617988843 chr13 115169878 3733521786 32.41751967471912 27.776670990068595 chr14 107349540 3307132225 30.80713922947411 28.551987982084714 chr15 102531392 3123653398 30.465336879460292 29.75072582887577 chr16 90354753 2922249791 32.34195981920287 45.049465876413876 chr17 81195210 2552235144 31.433321546923764 34.46250613115272 chr18 78077248 2917295667 37.36422250692033 29.076617544263712 chr19 59128983 1622477017 27.439623255485387 48.85228661286814 chr20 63025520 2360976659 37.46064544965277 30.805174340208016 chr21 48129895 1300581243 27.0223162340163 36.63815611023036 chr22 51304566 1146245401 22.341976365222543 28.765260108563666 chrMT 16571 648856629 39156.15406432925 15175.898988152943 chrX 155270560 3210521683 20.676950498536232 17.247336445011463 chrY 59373566 548416490 9.23671133379457 25.803311661459535