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
A19 F57 I0 R1	30	35.6	800162	95.7%	765755	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,343,438	C→T	37.1%	intergenic (+114/+250)	USA300HOU_RS11955 → / ← aldC_1	65 kDa membrane protein/Alpha‑acetolactate decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,343,438	0	C	T	37.1%	23.3 / 21.9	32	intergenic (+114/+250)	USA300HOU_RS11955/aldC_1	65 kDa membrane protein/Alpha‑acetolactate decarboxylase
Reads supporting (aligned to +/- strand): ref base C (8/12); new base T (6/6); total (14/18)
Fisher's exact test for biased strand distribution p-value = 7.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACG  >  USA300TCH1516_ALE/2343305‑2343569

tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTGGGAAATGATGGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTa                                                                                                                              >  2:382612/1‑141 (MQ=255)

  cAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTaaa                                                                                                                            >  1:114252/1‑141 (MQ=255)

    aaTTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAAtt                                                                                                                          >  2:78953/1‑141 (MQ=255)

                    taatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACTCGACGGAATTTTATATGAGTGTGTAc                                                                                                          <  1:293438/141‑1 (MQ=255)

                       tttGAAAATAGTTTTATAGGGCAAGCGCTGAAACATTGGCGTTTGTATTTTTAGTTACAGCAATTGTAAATTGATGCTGTTTTCTTGTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACcac                                                                                                       <  1:78953/141‑1 (MQ=255)

                             aagaGTTGTATAGGGCAAGCGCTTGAAAAGTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAACAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                 <  2:173900/138‑1 (MQ=255)

                             aaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGATACACGGTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                 <  1:171456/141‑1 (MQ=255)

                              aTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATGGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTtat                                                                                                <  1:307919/141‑1 (MQ=255)

                               tAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTtata                                                                                               >  1:23375/1‑141 (MQ=255)

                                             aaccgcAGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCCTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACa                                                                                 <  2:246896/138‑1 (MQ=255)

                                              aGCGCTGAAAAATGGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTTTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTGATATGAGTGTGTACCACAATTTATAATCTAAACATAAcgg                                                                                <  2:29126/141‑3 (MQ=255)

                                                  cTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCaaa                                                                            >  1:337620/1‑141 (MQ=255)

                                                     aaaaaTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAtct                                                                         <  2:28742/141‑1 (MQ=255)

                                                         aTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATCTATAATCTAAACATAACAGCAAATCTCaaa                                                                     <  1:111007/141‑1 (MQ=255)

                                                                        tttAGTTAGTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCtaat                                                      <  1:245545/141‑1 (MQ=255)

                                                                           ggTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATaaa                                                   <  1:196006/140‑1 (MQ=255)

                                                                                      ttGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCacta                                        <  2:23375/141‑1 (MQ=255)

                                                                                        gTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCactact                                      >  1:49581/1‑141 (MQ=255)

                                                                                           aaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAGATTTTAGATGAGTGTGTACCACAATTTATCATATAACCCGTACAGCAAATCTCAGATATCTGGAACCTAATGAATCCCCCCACTAATGCt                                   >  1:351321/1‑141 (MQ=255)

                                                                                           aaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCt                                   <  1:221984/141‑1 (MQ=255)

                                                                                               attGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATa                               <  1:44982/141‑1 (MQ=255)

                                                                                                     gttTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAg                         >  1:100400/1‑141 (MQ=255)

                                                                                                     gttTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATCCGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAg                         >  1:154910/1‑141 (MQ=255)

                                                                                                      tttGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTTCTAATAGTGAAgg                        <  1:99301/141‑1 (MQ=255)

                                                                                                               cGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCAGAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTAGTGCTAATAGTGAGGGGatttatat               >  2:171649/1‑139 (MQ=255)

                                                                                                               cGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATCTCTGGAACCTAATAAATCCCCTCACTACCGCTAATAGTGAAGGGatttattt               >  2:69118/1‑141 (MQ=255)

                                                                                                                 tagtaACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATATTGAAGGGAtttatttta             >  1:178527/1‑141 (MQ=255)

                                                                                                                  agtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGAtttattttat            >  2:238070/1‑141 (MQ=255)

                                                                                                                    taACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTttatta          <  2:312818/141‑1 (MQ=255)

                                                                                                                    taACAGAGTGGCCCATACCATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTttatta          <  2:106028/141‑1 (MQ=255)

                                                                                                                      aCAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACt        >  2:305332/1‑141 (MQ=255)

                                                                                                                            tGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAATCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTGTATTACTTAGACg  <  2:348509/141‑1 (MQ=255)

TACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACG  >  USA300TCH1516_ALE/2343305‑2343569

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A