BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231726.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,533,045 number of mapped reads = 5,164,275 (93.34%) number of supplementary alignments = 44,129 (0.8%) number of secondary alignments = 0 number of mapped bases = 351,011,562 bp number of sequenced bases = 350,879,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 601,786 duplication rate = 5.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4966 >>>>>>> ACTG content number of A's = 92,832,294 bp (26.46%) number of C's = 63,776,294 bp (18.18%) number of T's = 101,439,356 bp (28.91%) number of G's = 92,755,375 bp (26.44%) number of N's = 76,506 bp (0.02%) GC percentage = 44.61% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,298,612 number of insertions = 23,635 mapped reads with insertion percentage = 0.45% number of deletions = 79,469 mapped reads with deletion percentage = 1.52% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.1134X std coverageData = 38.3236X There is a 7.01% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.12% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% 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 27793472 0.11150813542005177 1.832214926932988 chr2 243199373 47636980 0.1958762451250234 136.69152024530402 chr3 198022430 21407819 0.10810805119399858 0.4628285022270004 chr4 191154276 21351185 0.11169608887012289 0.4886721931593516 chr5 180915260 16811992 0.09292744017281904 0.43781766525361376 chr6 171115067 16725280 0.09774288315592922 0.5610792959074593 chr7 159138663 29150805 0.1831786471650827 2.093389940655537 chr8 146364022 16793807 0.11473999395835133 0.9592407602680408 chr9 141213431 12206230 0.08643816606934505 0.7348652012606379 chr10 135534747 15787925 0.11648618047739448 0.7142841761115657 chr11 135006516 8273275 0.06128056071012158 0.6146286731915239 chr12 133851895 4784507 0.0357447834414298 0.2858865240149837 chr13 115169878 16847195 0.14628126114712042 0.5479552924211911 chr14 107349540 10176280 0.09479574854256478 0.570308508482912 chr15 102531392 7779735 0.07587661542720497 0.3887083441062701 chr16 90354753 8936097 0.09890013201629802 0.5167779645282504 chr17 81195210 10034070 0.12357958061811775 0.6230080483675736 chr18 78077248 12259239 0.15701423031713413 1.4265475968251535 chr19 59128983 10339679 0.17486651174095114 1.2978590267962662 chr20 63025520 10552438 0.16743119295168052 0.6149867889138333 chr21 48129895 8381512 0.1741435754223025 0.6435640003923243 chr22 51304566 2871341 0.055966578101450074 0.3301747063994138 chrMT 16571 327601 19.76953714320198 12.831576103317161 chrX 155270560 13075241 0.08420940196261287 0.5283626904238498 chrY 59373566 707857 0.011922090042562039 0.22265637226527468