BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716772.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 = 1,034,413 number of mapped reads = 969,408 (93.72%) number of supplementary alignments = 21,621 (2.09%) number of secondary alignments = 0 number of mapped bases = 74,918,494 bp number of sequenced bases = 74,889,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,017 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9119 >>>>>>> ACTG content number of A's = 18,499,926 bp (24.7%) number of C's = 15,905,611 bp (21.24%) number of T's = 21,799,632 bp (29.11%) number of G's = 18,680,987 bp (24.94%) number of N's = 3,141 bp (0%) GC percentage = 46.18% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 490,861 number of insertions = 6,334 mapped reads with insertion percentage = 0.64% number of deletions = 14,262 mapped reads with deletion percentage = 1.45% homopolymer indels = 38.58% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2257X There is a 2.14% of reference with a coverageData >= 1X There is a 0.2% 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% 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 8088287 0.032450418649107395 0.39629195397249484 chr2 243199373 6699617 0.027547838291507438 0.2309403043739088 chr3 198022430 4590470 0.023181565845848878 0.1680940318637389 chr4 191154276 3868315 0.020236612441774517 0.20359001424560919 chr5 180915260 4360906 0.02410468857077065 0.1721314989224133 chr6 171115067 4835455 0.028258499293928336 0.1922744523601333 chr7 159138663 4744074 0.02981094543944987 0.29411022239738027 chr8 146364022 4571739 0.031235401552438893 0.24090287595720494 chr9 141213431 2181744 0.015449975151442925 0.15984342365903362 chr10 135534747 4103941 0.030279622685981774 0.29172800344658334 chr11 135006516 3284004 0.024324781479436147 0.2002455683181524 chr12 133851895 2653114 0.019821265884954413 0.1543300217400831 chr13 115169878 1399104 0.012148176452874249 0.11989424272173159 chr14 107349540 1391133 0.012958909744745995 0.13156044512758283 chr15 102531392 1375027 0.013410790326537261 0.12711252460466474 chr16 90354753 2789514 0.030872908257521328 0.2008714303418666 chr17 81195210 1394932 0.01717997896673954 0.15487870881332064 chr18 78077248 2178120 0.027896987352832928 0.24383828380445963 chr19 59128983 1895401 0.03205536276516036 0.3043928646330512 chr20 63025520 1288738 0.020447875717645805 0.16375613386487342 chr21 48129895 1136526 0.02361372282237474 0.19207262870296565 chr22 51304566 1207352 0.023533032128173544 0.1734580248532476 chrMT 16571 94811 5.721501418140124 4.486773299274776 chrX 155270560 4536594 0.029217348092259086 0.1951599149927729 chrY 59373566 249576 0.004203486784000812 0.1595461330308642