BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695928.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 7,641,988 number of mapped reads = 6,567,461 (85.94%) number of supplementary alignments = 162,313 (2.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,320,847 number of mapped paired reads (second in pair) = 3,246,614 number of mapped paired reads (both in pair) = 6,053,040 number of mapped paired reads (singletons) = 514,421 number of mapped bases = 553,538,693 bp number of sequenced bases = 553,321,639 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,992,818 duplication rate = 17.25% >>>>>>> Insert size mean insert size = 146,226.0838 std insert size = 3,701,985.8915 median insert size = 322 >>>>>>> Mapping quality mean mapping quality = 51.7831 >>>>>>> ACTG content number of A's = 146,581,837 bp (26.49%) number of C's = 101,234,107 bp (18.3%) number of T's = 177,943,288 bp (32.16%) number of G's = 127,385,266 bp (23.02%) number of N's = 177,141 bp (0.03%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 8,266,603 number of insertions = 45,826 mapped reads with insertion percentage = 0.69% number of deletions = 123,507 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.1788X std coverageData = 1.6336X There is a 7.9% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 1.99% of reference with a coverageData >= 3X There is a 1.22% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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% 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 50100273 0.20100360351760166 2.7402595001293544 chr2 243199373 47933902 0.19709714465423395 2.0915296578931137 chr3 198022430 36252114 0.18307074607659343 0.9130631954568516 chr4 191154276 37368457 0.19548847026576585 1.0064477553628504 chr5 180915260 37132144 0.20524605829270565 0.9868231489923779 chr6 171115067 31171688 0.1821679910863723 1.2372176110343474 chr7 159138663 33061438 0.20775239264137843 2.068126518940569 chr8 146364022 28068102 0.19176913572380513 2.6875653700175555 chr9 141213431 23466775 0.16617948330991264 1.4191196918993245 chr10 135534747 26499859 0.19552077667581436 1.5250748994668075 chr11 135006516 26145425 0.19366046746958496 1.4086321748352533 chr12 133851895 24602847 0.18380649000150504 0.9395454230648028 chr13 115169878 16210516 0.14075308823371332 0.8061202342936199 chr14 107349540 16810826 0.15659895701462717 0.9004617396034055 chr15 102531392 15926359 0.15533153982733405 0.8553410769356932 chr16 90354753 15907265 0.17605343904819262 0.9320370840880613 chr17 81195210 15751072 0.19399016272019 1.0926982500884153 chr18 78077248 14333150 0.18357652667266142 3.2907616314996515 chr19 59128983 10523214 0.17797048868572626 1.7826865424805554 chr20 63025520 11505487 0.1825528293935536 0.9736668676843341 chr21 48129895 7026984 0.14600040162148703 0.9404618561767037 chr22 51304566 6003340 0.11701375663132985 0.8348671329277517 chrMT 16571 862998 52.078812383078876 33.934260327700905 chrX 155270560 16558992 0.1066460506099804 0.8134839970074557 chrY 59373566 4315466 0.07268328804774839 0.9400388391268204