BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975201.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 5,382,046 number of mapped reads = 5,309,028 (98.64%) number of supplementary alignments = 90,052 (1.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,657,115 number of mapped paired reads (second in pair) = 2,651,913 number of mapped paired reads (both in pair) = 5,285,074 number of mapped paired reads (singletons) = 23,954 number of mapped bases = 721,343,632 bp number of sequenced bases = 720,768,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,186,854 duplication rate = 18.06% >>>>>>> Insert size mean insert size = 79,523.2163 std insert size = 2,635,561.5288 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.9995 >>>>>>> ACTG content number of A's = 213,943,577 bp (29.68%) number of C's = 142,146,653 bp (19.72%) number of T's = 216,862,724 bp (30.09%) number of G's = 147,745,532 bp (20.5%) number of N's = 70,393 bp (0.01%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 9,407,503 number of insertions = 164,406 mapped reads with insertion percentage = 2.88% number of deletions = 262,494 mapped reads with deletion percentage = 4.71% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.233X std coverageData = 4.5264X There is a 10.66% of reference with a coverageData >= 1X There is a 6.47% of reference with a coverageData >= 2X There is a 1.96% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 55322988 0.22195727247556185 5.359451241795379 chr2 243199373 49855947 0.20500031058879417 4.997801090677261 chr3 198022430 42039128 0.21229477892984144 0.8638604667512614 chr4 191154276 38299563 0.20035943637483683 3.135884063564389 chr5 180915260 61084711 0.3376426676223996 1.015199792811661 chr6 171115067 41339654 0.24158979524579213 2.234612975076525 chr7 159138663 35502634 0.22309244862764746 3.2203776911740767 chr8 146364022 31293486 0.2138058627549877 1.3830151626763456 chr9 141213431 24208841 0.17143440838853352 6.4193353804654185 chr10 135534747 42668312 0.3148145619071396 12.521331149516726 chr11 135006516 31738246 0.2350867716636729 2.680082419139728 chr12 133851895 29262618 0.2186193777831834 0.767256014192788 chr13 115169878 17791202 0.15447790957979482 0.6111866661689079 chr14 107349540 23017067 0.21441234866958908 0.8885221310718749 chr15 102531392 13697794 0.13359609903667358 0.5700190680669531 chr16 90354753 29332568 0.324637797416147 9.72146361703181 chr17 81195210 13856384 0.17065519012759497 4.011081553915641 chr18 78077248 20595238 0.26378027565725676 6.604050069556293 chr19 59128983 10599063 0.1792532606217834 2.8986502649952497 chr20 63025520 10592791 0.1680714574032868 1.2722344440887947 chr21 48129895 9162203 0.1903640762150011 1.7673790548422692 chr22 51304566 5244014 0.10221339753658573 0.5696588593079599 chrMT 16571 204970 12.369199203427675 7.956098838736644 chrX 155270560 78534362 0.5057904215712238 2.2920936384640678 chrY 59373566 6099848 0.10273676336031425 5.88859792931753