BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354857.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 17,927,626 number of mapped reads = 17,632,380 (98.35%) number of supplementary alignments = 209,151 (1.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,848,986 number of mapped paired reads (second in pair) = 8,783,394 number of mapped paired reads (both in pair) = 17,533,912 number of mapped paired reads (singletons) = 98,468 number of mapped bases = 2,546,587,060 bp number of sequenced bases = 2,545,327,820 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,392,331 duplication rate = 66.48% >>>>>>> Insert size mean insert size = 66,154.1821 std insert size = 2,711,056.6126 median insert size = 450 >>>>>>> Mapping quality mean mapping quality = 54.1221 >>>>>>> ACTG content number of A's = 731,036,449 bp (28.72%) number of C's = 534,666,940 bp (21.01%) number of T's = 738,903,496 bp (29.03%) number of G's = 540,707,493 bp (21.24%) number of N's = 13,442 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 23,572,352 number of insertions = 446,997 mapped reads with insertion percentage = 2.34% number of deletions = 425,176 mapped reads with deletion percentage = 2.29% homopolymer indels = 41.9% >>>>>>> Coverage mean coverageData = 0.8226X std coverageData = 14.7763X There is a 19.67% of reference with a coverageData >= 1X There is a 15.23% of reference with a coverageData >= 2X There is a 11.02% of reference with a coverageData >= 3X There is a 8.38% of reference with a coverageData >= 4X There is a 5.97% of reference with a coverageData >= 5X There is a 4.47% of reference with a coverageData >= 6X There is a 3.17% of reference with a coverageData >= 7X There is a 2.35% of reference with a coverageData >= 8X There is a 1.67% of reference with a coverageData >= 9X There is a 1.23% of reference with a coverageData >= 10X There is a 0.87% of reference with a coverageData >= 11X There is a 0.64% of reference with a coverageData >= 12X There is a 0.46% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% 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 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% 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 210927750 0.8462476408433903 29.36978497656393 chr2 243199373 222201072 0.913658079208946 17.2891207467195 chr3 198022430 162797768 0.8221178176633829 2.3318683495394508 chr4 191154276 172043519 0.9000244336673902 19.678460279077036 chr5 180915260 147924209 0.817643624976688 2.18644094848183 chr6 171115067 141481015 0.8268179855839346 4.309619407724076 chr7 159138663 136194944 0.8558256141689465 14.01222054275377 chr8 146364022 124256555 0.8489555923791162 4.626791134170477 chr9 141213431 112405272 0.7959956160260705 18.808392952658263 chr10 135534747 149256016 1.101238016845968 31.318454273020716 chr11 135006516 111831667 0.8283427371757375 5.006998975248617 chr12 133851895 109626527 0.8190136344352839 2.1616059415680273 chr13 115169878 75498648 0.6555416165327534 1.8979966262346861 chr14 107349540 76066608 0.7085881131861395 2.0840220394034654 chr15 102531392 71895804 0.7012077237769287 2.017570871744343 chr16 90354753 79746431 0.8825925405385149 5.921413180806133 chr17 81195210 71568750 0.8814405431059296 6.165763818771026 chr18 78077248 73671474 0.9435716023187702 16.530995226191454 chr19 59128983 49658727 0.8398373264765944 14.68234668671397 chr20 63025520 54805668 0.8695789895902485 6.146845119838174 chr21 48129895 36108185 0.7502236395903211 9.143674339947674 chr22 51304566 33618534 0.6552737235902161 2.891179077974255 chrMT 16571 15772079 951.7880031380122 211.10772883104744 chrX 155270560 69307289 0.4463646489070433 2.0431880495188603 chrY 59373566 37922549 0.638710987984114 19.64110419191183