Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F1 I1 R1	690	31.8	1836723	97.1%	1783458	80.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,697	(A)_6→7	pseudogene (266/2434 nt)	yqiG →	putative outer membrane usher protein YqiG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,691	1	.	A	95.2%	67.9 / ‑3.2	21	pseudogene (260/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (10/10); total (11/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑AAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATC  >  NC_000913/3187612‑3187760

ggTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTg                                                                         <  2:531425/80‑1 (MQ=255)

       aTTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑aaaaaaac                                                                <  2:531426/81‑3 (MQ=255)

          gATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑aaaaaaactc                                                              <  2:531428/80‑5 (MQ=255)

          gATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑aaaaaaactc                                                              <  2:531427/80‑5 (MQ=255)

                   aCTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCt                                                    >  2:531453/1‑81 (MQ=255)

                      gCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGAGGATTTTTTTG‑AAAAAACCTCACCAAACCCTGAt                                                 >  1:531457/1‑81 (MQ=255)

                        aGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCg                                               <  1:531430/81‑1 (MQ=255)

                           ttGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATg                                            >  1:531463/1‑81 (MQ=255)

                                 gACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGgttgt                                       >  1:531462/1‑80 (MQ=255)

                                  acacCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGgttgtt                                      <  1:531431/80‑1 (MQ=255)

                                    acCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTAcc                                   >  1:531449/1‑81 (MQ=255)

                                      cAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCt                                 <  2:531431/81‑1 (MQ=255)

                                         agCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATc                              >  2:531454/1‑81 (MQ=255)

                                          gCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATc                              >  2:531468/1‑80 (MQ=255)

                                            aaTTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaa                           <  1:531434/81‑1 (MQ=255)

                                            aaTTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCga                            >  2:531457/1‑80 (MQ=255)

                                            aaTTAACATTATTAGGATTTACTGATGAA‑TTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaa                          <  2:531432/81‑1 (MQ=255)

                                             aTTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaa                          <  2:531434/81‑1 (MQ=255)

                                                 aCATTATTAGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaag                       <  2:531435/80‑1 (MQ=255)

                                                    ttattaGGATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaagaaaa                   <  1:531437/81‑1 (MQ=255)

                                                          ggATTTACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAAt             <  1:531438/81‑1 (MQ=255)

                                                               tACTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACaa        >  1:531456/1‑81 (MQ=255)

                                                                 cTGATGAATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACt      >  2:531460/1‑81 (MQ=255)

                                                                    atgaATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTAt   >  1:531459/1‑81 (MQ=255)

                                                                     tgaATTTATTGAAAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTAtc  <  1:531439/81‑1 (MQ=255)

GGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑AAAAAA‑CTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATC  >  NC_000913/3187612‑3187760

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A