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
A17 F25 I0 R1	13	19.6	632057	98.4%	621944	146.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,985,002	G→T	100%	D126Y (GAT→TAT)	ygeG →	SycD‑like chaperone family TPR‑repeat‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,985,002	0	G	T	67.8%	15.8 / 21.5	25	D126Y (GAT→TAT)	ygeG	SycD‑like chaperone family TPR‑repeat‑containing protein
Reads supporting (aligned to +/- strand): ref base G (1/7); new base T (11/6); total (12/13)
Fisher's exact test for biased strand distribution p-value = 3.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.42e-03
Rejected as polymorphism: Not supported by required number of reads on both strands.

AAAGATTTTGCATCAGTATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTAAATTTGCTGGTT  >  CP009273/2984858‑2985150

aaaGATTTTGCATCAGTATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATaa                                                                                                                                                  >  1:240179/1‑149 (MQ=255)

            tCATTATGGCAGACCAAAAAGAATTATCATCAAGCATATGACCTGTACAAACGAACTAACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACgcaat                                                                                                                                            <  2:188867/143‑1 (MQ=255)

                tATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTGACTGTCAGATTGGGGCTAAAAATTTCTATAAACGAATGCGATGTTTc                                                                                                                                  >  1:105412/1‑149 (MQ=255)

                          cAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCAAatta                                                                                                                        >  1:74832/1‑149 (MQ=255)

                              aaGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTaa                                                                                                                    <  1:138425/149‑1 (MQ=255)

                                gAAATATCCACCAGCATACGCCCTTTACAAACTAAGTTACAATTACTTCCCGTATGACCACTATTCAGTTATTTATCGTATCGGTCAATCTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCCCatta                                                                                                                        <  2:35770/143‑1 (MQ=255)

                                    tatCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTATATGACATTATTACCAAGtg                                                                                                              >  1:59857/1‑149 (MQ=255)

                                       caacaaGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGa                                                                                                           <  1:173346/149‑1 (MQ=255)

                                             gCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGa                                                                                                           <  2:275817/143‑1 (MQ=255)

                                               atatGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAAGGCAATGTTTCTATCACATTATTAACAATTGTGAgg                                                                                                         <  2:176313/143‑1 (MQ=255)

                                                           cAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAAGATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTa                                                                                             <  2:119742/143‑1 (MQ=255)

                                                              aCTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAg                                                                                    <  1:44476/149‑1 (MQ=255)

                                                                tAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAgcg                                                                                  >  1:327575/1‑149 (MQ=255)

                                                                tAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAacg                                                                                  >  1:182129/1‑149 (MQ=255)

                                                                   gTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTaaa                                                                                     <  2:160338/143‑1 (MQ=255)

                                                                   gTTACAACTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTaaa                                                                                     <  2:256290/143‑1 (MQ=255)

                                                                     tACAATTACTTCCCGTATGATGCCTATTCGGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAgga                                                                             >  1:328661/1‑148 (MQ=255)

                                                                              ttCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCAAATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCata                                                                          >  2:292110/1‑143 (MQ=255)

                                                                                             tATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTaaa                                                           >  2:154864/1‑143 (MQ=255)

                                                                                                               aTGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGCTGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATACTTCAGAAAATAATGGCTa                                   >  1:139523/1‑149 (MQ=255)

                                                                                                                  ggTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGc                                <  1:134458/149‑1 (MQ=255)

                                                                                                                               ttGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAAAAATTGTGAGGATGATAGTGTTCAGAGGAAAGCGCAGGCATATATTGAAATCTTAAACGATAATTAAGAAGATAATGGCTAAGCATTACaa                         >  2:263986/1‑143 (MQ=255)

                                                                                                                                    gCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATACTGGCCAAGCATTACAATCAtt                    <  2:257395/143‑1 (MQ=255)

                                                                                                                                      tAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTaaa            <  1:176377/149‑1 (MQ=255)

                                                                                                                                      tAAAAATATCGATAACGCAAGGCAATGTTTATATCAGATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGGTAGTTCAGAAGATAGTGGCTAAGCATTACAATGATTTTGGTaaa            >  1:142868/1‑149 (MQ=255)

                                                                                                                                                gATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGGTTGAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTAAATTTGCTGGtt  <  1:76588/149‑1 (MQ=255)

AAAGATTTTGCATCAGTATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTAAATTTGCTGGTT  >  CP009273/2984858‑2985150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A