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
A23 F59 I0 R1	88	34.1	751148	93.4%	701572	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,343,438	C→T	61.5%	intergenic (+114/+250)	USA300HOU_2200 → / ← alsD	hypothetical protein/acetolactate decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,343,438	0	C	T	61.5%	11.7 / 22.4	26	intergenic (+114/+250)	USA300HOU_2200/alsD	hypothetical protein/acetolactate decarboxylase
Reads supporting (aligned to +/- strand): ref base C (7/3); new base T (8/8); total (15/11)
Fisher's exact test for biased strand distribution p-value = 4.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.10e-01

AAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTAATTAT  >  CP000730/2343308‑2343576

aaaTTGTAGTTAAATAAGAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAAATATTGTTGTTTTCTTCTCGTAGTAACAGATTGGACTATACAATAGTAAAt                                                                                                                                  >  2:168736/1‑141 (MQ=255)

             ataataatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAgtgt                                                                                                                     >  1:9553/1‑141 (MQ=255)

                 ttatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAATTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTAc                                                                                                                 <  2:94058/139‑1 (MQ=255)

                 taatTTGAAAATTGTTTTATAGGGCAAGCGCGGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAGATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTAc                                                                                                                 <  2:73176/141‑1 (MQ=255)

                 aaatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTAc                                                                                                                 <  1:133213/140‑1 (MQ=255)

                  aatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTAcc                                                                                                                >  2:85795/1‑141 (MQ=255)

                     ttGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACcaca                                                                                                             <  2:9553/141‑1 (MQ=255)

                       gAAAATAGTTTTATAGGGCCAGCGCTGAAACATTGGCGTTCTTTTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAAt                                                                                                           <  2:166819/141‑1 (MQ=255)

                              gTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATGATAGTAAATTTTATATGAGTGTGTACCACAATTTATAAt                                                                                                    >  1:167990/1‑141 (MQ=255)

                                tttATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGGGTGTACCACAATTTATAATCt                                                                                                  >  1:29602/1‑141 (MQ=255)

                                        gCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTATCGTAGTAACAGATTGGCCTGTTTCGTGTGTAATAGTTTATGAGCGTGTACTACAATGTATAATCTAAACATaa                                                                                          >  1:269522/1‑141 (MQ=255)

                                            gcgcTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGc                                                                                      >  1:56404/1‑141 (MQ=255)

                                                 gAAAAATTGGCGGTTGTCTTTTTAGTTATTGAACTTGTAAATGATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAtc                                                                                 <  2:355286/141‑1 (MQ=255)

                                                              ttGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGa                                                                    <  1:126639/141‑1 (MQ=255)

                                                                 tCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTGTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAACCTCAAATATCTGGAAcc                                                                 <  1:362623/141‑1 (MQ=255)

                                                                  cTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCt                                                                <  1:50231/141‑1 (MQ=255)

                                                                                          ttattGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTaa                                        >  2:286364/1‑141 (MQ=255)

                                                                                           tattGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAAt                                       <  1:58638/141‑1 (MQ=255)

                                                                                                         tctcGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTACTAGTGAAGGGatttt                         >  1:98476/1‑140 (MQ=255)

                                                                                                           tcGTAGTAACAGATTGGCCTATATAATAGTAAATTTCATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCGTCACTACTGCTAATAGTGAAGGGatttatt                       >  2:125338/1‑141 (MQ=255)

                                                                                                               agtaACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATCTCAGGAACCTAATAAATCCAATAACTACTGCTAATAGTGAAGGGAtttattttat                   >  1:329115/1‑141 (MQ=255)

                                                                                                                          ggCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGt        >  2:97869/1‑141 (MQ=255)

                                                                                                                           gCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTTCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTa       <  2:2733/141‑1 (MQ=255)

                                                                                                                            ccTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTaa      >  2:227269/1‑141 (MQ=255)

                                                                                                                            ccTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCACATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTCATTTTATTACTTAgcagtta      >  1:174110/1‑135 (MQ=255)

                                                                                                                                aaCAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCGAATCTCAAATATCTGGAACCTAATAAATCACCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTAATtat  >  2:190995/2‑141 (MQ=255)

AAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACGTAATTAT  >  CP000730/2343308‑2343576

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