BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173960.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 = 32,155,866 number of mapped reads = 31,313,814 (97.38%) number of supplementary alignments = 4,831,563 (15.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,672,860 number of mapped paired reads (second in pair) = 15,640,954 number of mapped paired reads (both in pair) = 30,751,418 number of mapped paired reads (singletons) = 562,396 number of mapped bases = 3,555,123,195 bp number of sequenced bases = 3,552,687,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,247,909 duplication rate = 66.44% >>>>>>> Insert size mean insert size = 1,465,327.0549 std insert size = 11,109,355.4246 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 52.1651 >>>>>>> ACTG content number of A's = 1,052,451,620 bp (29.62%) number of C's = 711,544,858 bp (20.03%) number of T's = 1,045,153,844 bp (29.42%) number of G's = 743,511,232 bp (20.93%) number of N's = 25,922 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 31,842,410 number of insertions = 418,386 mapped reads with insertion percentage = 1.28% number of deletions = 1,030,821 mapped reads with deletion percentage = 3.21% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 1.1484X std coverageData = 18.8799X There is a 20.87% of reference with a coverageData >= 1X There is a 16.57% of reference with a coverageData >= 2X There is a 13.16% of reference with a coverageData >= 3X There is a 10.85% of reference with a coverageData >= 4X There is a 8.56% of reference with a coverageData >= 5X There is a 7.1% of reference with a coverageData >= 6X There is a 5.58% of reference with a coverageData >= 7X There is a 4.74% of reference with a coverageData >= 8X There is a 3.75% of reference with a coverageData >= 9X There is a 3.27% of reference with a coverageData >= 10X There is a 2.6% of reference with a coverageData >= 11X There is a 2.31% of reference with a coverageData >= 12X There is a 1.83% of reference with a coverageData >= 13X There is a 1.64% of reference with a coverageData >= 14X There is a 1.3% of reference with a coverageData >= 15X There is a 1.16% of reference with a coverageData >= 16X There is a 0.92% of reference with a coverageData >= 17X There is a 0.83% of reference with a coverageData >= 18X There is a 0.66% of reference with a coverageData >= 19X There is a 0.6% of reference with a coverageData >= 20X There is a 0.48% of reference with a coverageData >= 21X There is a 0.43% of reference with a coverageData >= 22X There is a 0.35% of reference with a coverageData >= 23X There is a 0.32% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 293803482 1.1787472417170026 10.722929857967962 chr2 243199373 320605099 1.3182809439233216 62.94134654989231 chr3 198022430 239389661 1.208901744110503 3.47323572832662 chr4 191154276 235379384 1.2313581936299454 9.00817464368094 chr5 180915260 214876228 1.1877175424560649 3.456597261189591 chr6 171115067 208689318 1.219584702029775 5.786751402240812 chr7 159138663 194978924 1.225214038652568 7.485052566374671 chr8 146364022 179491813 1.226338348368153 9.447442471130048 chr9 141213431 151351527 1.0717927177904203 8.429324435160106 chr10 135534747 173661492 1.28130605504432 10.711479610320142 chr11 135006516 164149257 1.2158617366290676 4.3932036498610225 chr12 133851895 163314817 1.220115837732443 4.40229177601315 chr13 115169878 113726500 0.9874674001130747 3.1042881000529268 chr14 107349540 110879894 1.032886531232458 3.5365249481795265 chr15 102531392 105898643 1.0328411712190546 3.8262639100055926 chr16 90354753 111156966 1.230228209466745 6.1939512629004 chr17 81195210 104748301 1.2900798088951306 4.9765972992542435 chr18 78077248 94943198 1.2160161946281713 11.037619491558752 chr19 59128983 73687143 1.2462102214746362 6.858259021808298 chr20 63025520 77582866 1.2309754207501977 4.57489309444246 chr21 48129895 50164447 1.0422721055177868 6.027110000228903 chr22 51304566 46973678 0.915584745420125 4.114519067497846 chrMT 16571 5285811 318.9796029207652 207.34537500874143 chrX 155270560 92623386 0.596528962090431 2.7133767484674953 chrY 59373566 27761360 0.46757103994730587 7.673735788824342