BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174032.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 = 3,798,912 number of mapped reads = 3,689,247 (97.11%) number of supplementary alignments = 354,739 (9.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,850,693 number of mapped paired reads (second in pair) = 1,838,554 number of mapped paired reads (both in pair) = 3,616,986 number of mapped paired reads (singletons) = 72,261 number of mapped bases = 433,325,357 bp number of sequenced bases = 433,091,842 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,812,266 duplication rate = 63.52% >>>>>>> Insert size mean insert size = 901,595.4112 std insert size = 8,521,570.5409 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.6316 >>>>>>> ACTG content number of A's = 130,028,178 bp (30.02%) number of C's = 85,172,761 bp (19.67%) number of T's = 129,775,037 bp (29.96%) number of G's = 88,110,875 bp (20.34%) number of N's = 4,991 bp (0%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 4,523,394 number of insertions = 44,556 mapped reads with insertion percentage = 1.17% number of deletions = 92,382 mapped reads with deletion percentage = 2.45% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.14X std coverageData = 2.0595X There is a 3.05% of reference with a coverageData >= 1X There is a 2.37% of reference with a coverageData >= 2X There is a 1.81% of reference with a coverageData >= 3X There is a 1.47% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.88% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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% of reference with a coverageData >= 33X There is a 0% 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 33579936 0.13472358008688773 1.5102553060606518 chr2 243199373 37722964 0.15511127160677343 5.891954229690919 chr3 198022430 34642126 0.17494041457828793 1.2057840577260632 chr4 191154276 23163178 0.12117530658848563 1.1282347412182385 chr5 180915260 22112669 0.12222666567762167 0.9894809025005405 chr6 171115067 22917344 0.13392943357816645 1.1550328249115824 chr7 159138663 25111257 0.1577948219911839 1.479173991573425 chr8 146364022 26641783 0.18202412475382782 1.517448793678801 chr9 141213431 18384432 0.13018897614632705 1.21496325458817 chr10 135534747 23396349 0.17262251575974094 2.057003885698325 chr11 135006516 15747797 0.11664471809642137 0.9801457818963607 chr12 133851895 18302451 0.13673658486493598 1.053648591717846 chr13 115169878 11188895 0.09715122733741195 0.883259598268898 chr14 107349540 13376754 0.12460932762264282 0.9955179645259472 chr15 102531392 14867674 0.1450060679952536 1.0698168445381464 chr16 90354753 14324072 0.15853147205216753 1.336021211810082 chr17 81195210 17809211 0.21933819741336957 1.4083253058726561 chr18 78077248 8287941 0.10615052671938437 1.6504444522806525 chr19 59128983 6958560 0.11768441882384481 1.2533651969301896 chr20 63025520 18547067 0.2942786826669578 1.6359554363324498 chr21 48129895 5382381 0.11183030837694535 0.9680584619628486 chr22 51304566 3267681 0.0636918164359874 0.6755672227726943 chrMT 16571 1062282 64.10488202281094 49.81615706032011 chrX 155270560 15706718 0.10115708992097407 0.9002652726556776 chrY 59373566 823835 0.013875450903521611 0.5567850118856633