BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472511.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 = 14,596,680 number of mapped reads = 14,406,540 (98.7%) number of supplementary alignments = 49,316 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,229,795 number of mapped paired reads (second in pair) = 7,176,745 number of mapped paired reads (both in pair) = 14,306,598 number of mapped paired reads (singletons) = 99,942 number of mapped bases = 1,417,358,802 bp number of sequenced bases = 1,417,173,757 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,845,507 duplication rate = 44.91% >>>>>>> Insert size mean insert size = 28,072.2388 std insert size = 1,642,041.5345 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 54.9736 >>>>>>> ACTG content number of A's = 396,412,052 bp (27.97%) number of C's = 313,942,793 bp (22.15%) number of T's = 394,231,969 bp (27.82%) number of G's = 312,370,037 bp (22.04%) number of N's = 216,906 bp (0.02%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 8,737,820 number of insertions = 76,856 mapped reads with insertion percentage = 0.53% number of deletions = 74,235 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 0.4578X std coverageData = 17.3246X There is a 4.63% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 151277357 0.6069287065086189 19.6716926518814 chr2 243199373 88016065 0.36190909505346464 13.484919576408434 chr3 198022430 195228992 0.985893325316733 25.3678732361852 chr4 191154276 61577610 0.3221356659581081 12.619859495593177 chr5 180915260 101679320 0.5620273270480334 25.68886115444731 chr6 171115067 94054412 0.5496559341556989 18.306774794653222 chr7 159138663 48400598 0.3041410370526991 11.208694408254912 chr8 146364022 53113293 0.36288489667221635 11.852409421145833 chr9 141213431 68144252 0.4825621154973566 11.154181617825861 chr10 135534747 49337639 0.36402206882047744 16.521161015495657 chr11 135006516 68018959 0.5038198230372821 17.729446918275688 chr12 133851895 60022716 0.44842634465503833 12.22676417254428 chr13 115169878 35160421 0.3052918142363579 11.474989299270023 chr14 107349540 40351499 0.37588888597007497 24.37333829092431 chr15 102531392 32229227 0.31433521355098737 11.731679051799786 chr16 90354753 38537376 0.4265118847704669 12.69365562790519 chr17 81195210 55867838 0.6880681508182565 28.740550315398377 chr18 78077248 23121454 0.2961356168701028 16.37505292325795 chr19 59128983 26811655 0.45344353377429136 14.022597256883035 chr20 63025520 32387076 0.5138724123180578 23.530380944986437 chr21 48129895 4997763 0.10383905886351923 2.8337127912681117 chr22 51304566 16238451 0.31651083453273926 12.603100327423148 chrMT 16571 1245 0.07513125339448434 0.3059821946867546 chrX 155270560 70836355 0.4562124011145448 17.10001276212655 chrY 59373566 1947229 0.03279622787016027 1.3938216729266522