BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975256.sorted.bam outfile = /mainsd/zhouyj/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 = 162,552,378 number of mapped reads = 162,034,198 (99.68%) number of supplementary alignments = 307,428 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 81,011,320 number of mapped paired reads (second in pair) = 81,022,878 number of mapped paired reads (both in pair) = 161,816,332 number of mapped paired reads (singletons) = 217,866 number of mapped bases = 14,845,145,061 bp number of sequenced bases = 14,840,359,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,682,230 duplication rate = 47.89% >>>>>>> Insert size mean insert size = 74,356.4998 std insert size = 2,697,009.4718 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 55.854 >>>>>>> ACTG content number of A's = 3,839,844,475 bp (25.87%) number of C's = 3,317,819,076 bp (22.36%) number of T's = 4,042,467,814 bp (27.24%) number of G's = 3,639,814,993 bp (24.53%) number of N's = 412,642 bp (0%) GC percentage = 46.88% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 95,586,438 number of insertions = 1,294,016 mapped reads with insertion percentage = 0.79% number of deletions = 3,359,866 mapped reads with deletion percentage = 2.05% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 4.7954X std coverageData = 61.7645X There is a 28.91% of reference with a coverageData >= 1X There is a 17.68% of reference with a coverageData >= 2X There is a 11.31% of reference with a coverageData >= 3X There is a 8.23% of reference with a coverageData >= 4X There is a 6.21% of reference with a coverageData >= 5X There is a 5.04% of reference with a coverageData >= 6X There is a 4.22% of reference with a coverageData >= 7X There is a 3.68% of reference with a coverageData >= 8X There is a 3.29% of reference with a coverageData >= 9X There is a 3% of reference with a coverageData >= 10X There is a 2.79% of reference with a coverageData >= 11X There is a 2.62% of reference with a coverageData >= 12X There is a 2.48% of reference with a coverageData >= 13X There is a 2.37% of reference with a coverageData >= 14X There is a 2.28% of reference with a coverageData >= 15X There is a 2.2% of reference with a coverageData >= 16X There is a 2.14% of reference with a coverageData >= 17X There is a 2.08% of reference with a coverageData >= 18X There is a 2.02% of reference with a coverageData >= 19X There is a 1.98% of reference with a coverageData >= 20X There is a 1.93% of reference with a coverageData >= 21X There is a 1.89% of reference with a coverageData >= 22X There is a 1.85% of reference with a coverageData >= 23X There is a 1.82% of reference with a coverageData >= 24X There is a 1.79% of reference with a coverageData >= 25X There is a 1.76% of reference with a coverageData >= 26X There is a 1.73% of reference with a coverageData >= 27X There is a 1.7% of reference with a coverageData >= 28X There is a 1.67% of reference with a coverageData >= 29X There is a 1.65% of reference with a coverageData >= 30X There is a 1.63% of reference with a coverageData >= 31X There is a 1.6% of reference with a coverageData >= 32X There is a 1.58% of reference with a coverageData >= 33X There is a 1.56% of reference with a coverageData >= 34X There is a 1.54% of reference with a coverageData >= 35X There is a 1.52% of reference with a coverageData >= 36X There is a 1.5% of reference with a coverageData >= 37X There is a 1.48% of reference with a coverageData >= 38X There is a 1.47% of reference with a coverageData >= 39X There is a 1.45% of reference with a coverageData >= 40X There is a 1.43% of reference with a coverageData >= 41X There is a 1.41% of reference with a coverageData >= 42X There is a 1.4% of reference with a coverageData >= 43X There is a 1.38% of reference with a coverageData >= 44X There is a 1.37% of reference with a coverageData >= 45X There is a 1.35% of reference with a coverageData >= 46X There is a 1.34% of reference with a coverageData >= 47X There is a 1.33% of reference with a coverageData >= 48X There is a 1.31% of reference with a coverageData >= 49X There is a 1.3% of reference with a coverageData >= 50X There is a 1.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1724494626 6.918717470316754 81.0478347234837 chr2 243199373 996255311 4.096455096535138 51.182643241399795 chr3 198022430 779515472 3.936500890328434 49.68376604996029 chr4 191154276 494335201 2.5860535863712513 38.84647576406443 chr5 180915260 685273866 3.7878168265076146 49.86009948934337 chr6 171115067 1184849469 6.9242848673284865 87.46866467690467 chr7 159138663 761244273 4.78352814237229 64.53403070359778 chr8 146364022 463805107 3.1688464191015466 40.828281107721395 chr9 141213431 567126088 4.016091698812983 50.50474358914734 chr10 135534747 618914497 4.5664636611598945 58.868446782967204 chr11 135006516 922891303 6.835901927874355 76.72629844795986 chr12 133851895 893576951 6.675863281577 77.85421359235156 chr13 115169878 408181307 3.544167225739355 52.404391862772385 chr14 107349540 494214147 4.603784487572094 61.13065622777362 chr15 102531392 449846690 4.387404493640347 53.32973208526536 chr16 90354753 569352804 6.301304415053849 71.89191723909045 chr17 81195210 685490735 8.442502150065256 84.50667074254811 chr18 78077248 315991950 4.047170694335948 55.81690893907855 chr19 59128983 510819675 8.639074259065136 80.56480593463344 chr20 63025520 430682234 6.833457843743297 78.67227116397093 chr21 48129895 153749499 3.194469861195417 49.53393750016158 chr22 51304566 228770961 4.459076040132568 54.820574513091856 chrMT 16571 329617 19.891195461951604 19.803286787196683 chrX 155270560 490986761 3.162136859685442 43.961892490827395 chrY 59373566 14446517 0.24331563645680301 5.408338872212981