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
A8 F1 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,842,141	A→G	intergenic (‑6/‑230)	ynjH ← / → gdhA	DUF1496 family protein/glutamate dehydrogenase, NADP‑specific

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,842,141	0	A	G	97.1%	110.4 / ‑4.4	34	intergenic (‑6/‑230)	ynjH/gdhA	DUF1496 family protein/glutamate dehydrogenase, NADP‑specific
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (20/13); total (21/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

TGCGCTGACTGCCCGCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAACTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTCCTGGGTCATTTTTTTCTTGC  >  NC_000913/1842008‑1842272

tGCGCTGACTGCCCGCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCt                                                                                                                                >  2:38137/1‑139 (MQ=255)

  cgcTGACTGCCCGCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAGATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTa                                                                                                                              >  1:640527/1‑139 (MQ=255)

  cgcTGACTGCCCGCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTa                                                                                                                              >  1:407322/1‑139 (MQ=255)

  cgcTGACTGCCCCCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTa                                                                                                                              <  2:640527/139‑1 (MQ=255)

    cTGACTGCCCGCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAAc                                                                                                                            <  2:554429/139‑1 (MQ=255)

                                                                aaTGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTc                                                                                                                                  >  1:439747/1‑73 (MQ=255)

                                                                aaTGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTc                                                                                                                                  <  2:439747/73‑1 (MQ=255)

                                                                       gTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGa                                                                                                        >  1:640837/1‑92 (MQ=255)

                                                                       gTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGCAGCTCCTTAACGTTATTGTCTCTGCTACTGa                                                                                                        <  2:640837/92‑1 (MQ=255)

                                                                            ccAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTa                                                    <  2:14252/139‑1 (MQ=255)

                                                                                tGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCAtt                                                          <  1:26880/129‑1 (MQ=255)

                                                                                tGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCAtt                                                          >  2:26880/1‑129 (MQ=255)

                                                                                tGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATgag                                                >  1:509585/1‑139 (MQ=255)

                                                                                                 cTAATACTACGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTaa                               >  1:326067/1‑139 (MQ=255)

                                                                                                         acGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCttt                       >  1:960194/1‑139 (MQ=255)

                                                                                                          tggCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTAct                                          <  2:980349/118‑1 (MQ=255)

                                                                                                          tggCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTAct                                          >  1:980349/2‑119 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTa                                                                                                            >  1:233378/1‑53 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTa                                                                                                            <  2:233378/53‑1 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCgg                                                                                           >  1:251749/1‑70 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCgg                                                                                           <  2:251749/70‑1 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTc                      >  1:566244/1‑139 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTc                      >  1:264437/1‑139 (MQ=255)

                                                                                                          cGGCGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTc                      >  2:1032445/1‑139 (MQ=255)

                                                                                                           ggCGAACAATGCTCGACTCACAGGGAGTTCCTTAACGTTATTGtctc                                                                                                                 <  1:701440/47‑1 (MQ=255)

                                                                                                           ggCGAACAATGCTCGACTCACAGGGAGTTCCTTAACGTTATTGtctc                                                                                                                 >  2:701440/1‑47 (MQ=255)

                                                                                                             cGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGtct                                                                                                                  <  2:55021/44‑1 (MQ=255)

                                                                                                             cGAACAATGCTCGACTCACAGGGAGCTCCTTAACGTTATTGtct                                                                                                                  >  1:55021/1‑44 (MQ=255)

                                                                                                                    tGCTCGACTCACAGGGAACTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTCCTGGGTCAtt            >  2:1044823/1‑139 (MQ=255)

                                                                                                                      cTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTa                                                                 >  1:614291/1‑84 (MQ=255)

                                                                                                                      cTCGACTCACAGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTa                                                                 <  2:614291/84‑1 (MQ=255)

                                                                                                                              acaGGGAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTCCTGGGTCATTTTTTTCTTGc  >  1:119996/1‑139 (MQ=255)

                                                                                                                                  ggAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCAtt                                                          <  1:91270/79‑1 (MQ=255)

                                                                                                                                  ggAGCTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCAtt                                                          >  2:91270/1‑79 (MQ=255)

TGCGCTGACTGCCCGCCTGAACTGAACACTTCTGGCGGTACGTTTACCTCCACGTCCGGACGATAATGCGGGTTAGCCAGTGCAATTAATGGAAATGCTAATACTACGGCGAACAATGCTCGACTCACAGGGAACTCCTTAACGTTATTGTCTCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTTTAGCGTCTGAGTTATCGCATTTGGTTATGAGATTACTCTCGTTATTAATTTGCTTTCCTGGGTCATTTTTTTCTTGC  >  NC_000913/1842008‑1842272

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A