BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173938.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,404,292 number of mapped reads = 4,294,025 (97.5%) number of supplementary alignments = 566,253 (12.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,150,173 number of mapped paired reads (second in pair) = 2,143,852 number of mapped paired reads (both in pair) = 4,224,732 number of mapped paired reads (singletons) = 69,293 number of mapped bases = 485,580,208 bp number of sequenced bases = 485,224,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,457,360 duplication rate = 64.38% >>>>>>> Insert size mean insert size = 1,226,403.9657 std insert size = 9,951,199.2008 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 52.5693 >>>>>>> ACTG content number of A's = 144,648,752 bp (29.81%) number of C's = 96,578,680 bp (19.9%) number of T's = 143,381,006 bp (29.55%) number of G's = 100,612,589 bp (20.74%) number of N's = 3,666 bp (0%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 4,272,135 number of insertions = 53,006 mapped reads with insertion percentage = 1.19% number of deletions = 149,083 mapped reads with deletion percentage = 3.39% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.1569X std coverageData = 2.9697X There is a 3.33% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 1.86% of reference with a coverageData >= 3X There is a 1.5% of reference with a coverageData >= 4X There is a 1.13% of reference with a coverageData >= 5X There is a 0.94% of reference with a coverageData >= 6X There is a 0.71% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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% 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 39330491 0.1577949569080512 1.4961922969956427 chr2 243199373 42316749 0.17400023889041852 9.437258091806703 chr3 198022430 31606458 0.15961049462932053 1.2221403779094293 chr4 191154276 34243148 0.1791388020009555 1.6338355891774494 chr5 180915260 30951025 0.17108023391724944 1.2738879230577003 chr6 171115067 29734525 0.17376918071159683 1.4176430381313059 chr7 159138663 27490124 0.1727432132567307 1.6451978289008564 chr8 146364022 25012635 0.17089332923633377 1.7555181769561803 chr9 141213431 21426512 0.1517314029428263 1.4762411064659229 chr10 135534747 23445616 0.1729860166411791 1.8320177691507522 chr11 135006516 21886693 0.1621158270612657 1.2657661143693606 chr12 133851895 21497157 0.16060405420483587 1.2442993296034206 chr13 115169878 15005568 0.13029073452695678 1.1063627870495865 chr14 107349540 14108531 0.13142609646953307 1.1047780573019503 chr15 102531392 14214224 0.13863289791286557 1.151561446415755 chr16 90354753 15390653 0.1703358427641322 1.4033748551793765 chr17 81195210 13230627 0.1629483685059747 1.2479849511225571 chr18 78077248 13476925 0.17261014373867276 1.8290662646648688 chr19 59128983 9364365 0.15837182587767493 1.311791740745377 chr20 63025520 11006753 0.1746396221720979 1.3140678081873487 chr21 48129895 6910745 0.14358529142853937 1.4048452924857722 chr22 51304566 6417429 0.12508494857943053 1.203409886807078 chrMT 16571 520653 31.419528091243738 29.206168030425623 chrX 155270560 13266238 0.08543949348801215 0.8929122481635761 chrY 59373566 3726364 0.06276133052207106 1.0327475712230767