BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,095,443 number of mapped reads = 1,586,868 (75.73%) number of supplementary alignments = 5,501 (0.26%) number of secondary alignments = 0 number of mapped bases = 87,843,224 bp number of sequenced bases = 87,817,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,512 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.2261 >>>>>>> ACTG content number of A's = 21,555,478 bp (24.55%) number of C's = 15,973,908 bp (18.19%) number of T's = 27,226,562 bp (31%) number of G's = 23,060,324 bp (26.26%) number of N's = 1,175 bp (0%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 459,101 number of insertions = 6,045 mapped reads with insertion percentage = 0.38% number of deletions = 16,188 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.16% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.2522X There is a 2.57% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 7381113 0.029613218095051404 0.297181094420129 chr2 243199373 8562132 0.03520622563447152 0.4506425635675675 chr3 198022430 5804589 0.029312785425368228 0.19311986312279047 chr4 191154276 4946391 0.025876433964783504 0.18870981596944758 chr5 180915260 4712490 0.02604805144684865 0.17730995280882333 chr6 171115067 4856236 0.028379943888868654 0.21128200979740228 chr7 159138663 4321168 0.027153476839251817 0.3772065908671151 chr8 146364022 7080267 0.04837436757511351 0.2696792210554816 chr9 141213431 3718988 0.02633593684158839 0.19928263580942496 chr10 135534747 4197764 0.030971865834522862 0.2760475906206249 chr11 135006516 2972892 0.02202035937287649 0.20027311949114568 chr12 133851895 4115051 0.03074331521417758 0.1942057968901332 chr13 115169878 2280871 0.019804405801315515 0.15848673920914244 chr14 107349540 2842364 0.026477654212584422 0.1845636715107202 chr15 102531392 2137490 0.020847176248226493 0.1621487028293754 chr16 90354753 2781242 0.03078135801002079 0.20245702354623846 chr17 81195210 3329614 0.041007517561688675 0.22935355606888705 chr18 78077248 2003540 0.025660996658078934 0.26247565249472254 chr19 59128983 2138607 0.03616850639896851 0.28308845939872385 chr20 63025520 2030719 0.03222058302731973 0.199638871927472 chr21 48129895 910465 0.018916829134989804 0.15544054445126168 chr22 51304566 1407308 0.027430463011810683 0.1835848318630191 chrMT 16571 13162 0.7942791623921308 1.048986804592994 chrX 155270560 3085905 0.019874372836679408 0.1766204052618319 chrY 59373566 212856 0.00358502974202358 0.09663316055524207