BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080660.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,464,046 number of mapped reads = 1,327,314 (90.66%) number of supplementary alignments = 10,915 (0.75%) number of secondary alignments = 0 number of mapped bases = 87,733,291 bp number of sequenced bases = 87,701,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,282 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4274 >>>>>>> ACTG content number of A's = 23,538,822 bp (26.84%) number of C's = 16,283,746 bp (18.57%) number of T's = 27,647,917 bp (31.52%) number of G's = 20,227,518 bp (23.06%) number of N's = 3,767 bp (0%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 598,472 number of insertions = 6,582 mapped reads with insertion percentage = 0.49% number of deletions = 19,649 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.6% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.2346X There is a 2.46% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 10695854 0.04291204554310819 0.24932465267260082 chr2 243199373 5944036 0.024441000511954445 0.346249222641574 chr3 198022430 5529341 0.027922801472540257 0.18658143950105793 chr4 191154276 3671780 0.019208463848331594 0.15707217842675084 chr5 180915260 4086468 0.022587746329414113 0.1684919371692905 chr6 171115067 5287012 0.03089740776596838 0.226440439656786 chr7 159138663 5438715 0.03417595006437876 0.46399160028428454 chr8 146364022 10241993 0.0699761653174576 0.3223533415297119 chr9 141213431 2704813 0.0191540774899804 0.17453081954071986 chr10 135534747 4143673 0.030572772604209014 0.20365651620801378 chr11 135006516 3724959 0.027590957165356374 0.19526733036328023 chr12 133851895 2797863 0.02090267754520771 0.16286907822964922 chr13 115169878 1759108 0.01527402850943369 0.1391680907348881 chr14 107349540 1752197 0.01632235219638575 0.14458354605322957 chr15 102531392 1675998 0.016346193758883132 0.15447440847527863 chr16 90354753 2218080 0.024548570234041812 0.1777574068924976 chr17 81195210 1582977 0.019495940708817674 0.15914657825255077 chr18 78077248 2887952 0.03698839385322598 0.24295019249483732 chr19 59128983 1446233 0.024458952727125376 0.1857966824726472 chr20 63025520 2290797 0.03634713366902804 0.21568381185992352 chr21 48129895 1258972 0.026157796521268123 0.183143708477303 chr22 51304566 863947 0.01683957330425522 0.14523768027654088 chrMT 16571 10022 0.6047915032285318 0.925268019163336 chrX 155270560 5547281 0.0357265472604723 0.21673329121305482 chrY 59373566 173220 0.002917459934948155 0.06536021930231928