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 F16 I1 R1	9	28.1	657842	93.6%	615740	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	97.7%	107.6 / ‑6.7	44	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (24/19); minor base C (0/1); total (24/20)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAT  >  USA300TCH1516_ALE/2279573‑2279834

ccGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTCAAACGTTGATTAACTTACGATTTATCATTTGCATCATCAGTTGCTGATGTTACtgttgt                                                                                                                            >  1:325003/1‑140 (MQ=255)

           ttaTTCTACTTCTTGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTTATTCATCTACACTATAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTg                                                                                                                 <  1:171593/138‑1 (MQ=255)

           tGATTCTACTTCTGGTTGACTAGTTTCATCGTTATCCTTTGTCGGACTGTTTGTTGATGCATCTACACTAGCATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTg                                                                                                                 <  2:185039/140‑1 (MQ=255)

              tttttcTTTTGGTTTATTTGTTACATCGTTATCCAATGGCGGACTGCTTGTGGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGCTGCTGATGTTCCTTTCGTTTCACCTGTTGCCg                                                                                                              <  1:14191/135‑1 (MQ=255)

                  aCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGATTTGTAATTAGCTTGAGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATc                                                                                                          >  1:256610/1‑140 (MQ=255)

                  aCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTGGCCGCATc                                                                                                          >  1:248311/1‑140 (MQ=255)

                  aCTTCGGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACATGTTGCCGCATc                                                                                                          >  1:93072/1‑140 (MQ=255)

                    ttCTGGTTTACTAGTTACAGCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCAc                                                                                                        <  1:37841/140‑1 (MQ=255)

                         gTTTACTAGTTACATCGTTATCCATTGTCGTTGTGTTTGTTGATGCATCTACACTAGAATTGTTATGAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACtatta                                                                                                   <  1:80351/140‑1 (MQ=255)

                               tAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGgt                                                                                             >  1:319206/1‑140 (MQ=255)

                                   tACATGGTTATCCATTGTCGGATTGTTTTTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCTTCAGTTTCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgttg                                                                                         <  2:213955/140‑1 (MQ=255)

                                    acctCGTTATTCCTTGTCGGACTATTCGGTGATGCAGCTACACTAGAACTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgttgt                                                                                        <  1:9521/137‑1 (MQ=255)

                                    aCATCCTTATACAGTGTCGGACTGTTTGTGGATGCATCTAAACTAAAATTGTTATTTGGTTGGGGTTTATCATTTGCATTATCAGTTGCTGATGTTATTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgttgt                                                                                        <  2:46551/140‑1 (MQ=255)

                                          ttATCCATTGTCGGACTGTTTGTTGATGCATCTACAATAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTAACATGTTGCAGCATCACTATTATTTTGAGTTGTCGgaga                                                                                  >  2:26233/1‑140 (MQ=255)

                                           tATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGaa                                                                                 >  1:250889/1‑140 (MQ=255)

                                           tATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGaa                                                                                 >  1:269642/1‑140 (MQ=255)

                                                    tCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCt                                                                        <  1:80443/140‑1 (MQ=255)

                                                     cGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCAATATTATTTGGTGTTGTCGGAAAAGCGTCGGCtt                                                                       >  2:15754/1‑140 (MQ=255)

                                                             tttttgATGTATCTACACTAGAACTGTGGCCAGTTTGCGGTTTATCATTTGCATCATCAGTTGCTTATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGTTGTTGTCGGAGAAGCGTCTGCTTTGCCATTa                                                               <  2:52373/137‑1 (MQ=255)

                                                             ttgctaaTGCTTCTACACTAAAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGTTGTTGTTACGGTTGTTTGTCCTGTTGCCGCATCACTATTATTTTGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTa                                                               <  2:84044/134‑1 (MQ=255)

                                                              tggtgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAg                                                              <  1:306901/137‑1 (MQ=255)

                                                                ttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCt                                                            >  2:38575/1‑140 (MQ=255)

                                                                ttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCt                                                            >  2:256940/1‑140 (MQ=255)

                                                                ttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTACATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCt                                                            >  2:168193/1‑140 (MQ=255)

                                                                               tAGAATTGTTATTAGCTTGCAGTTTATCCTTTGCATCATCAGTTGCTGATGTTACTGATGTTTAACATGTTGCCGCATCACTATTATTTCTTGTTGTTGGAGACGCTTCTGTTTTCCCATTAGCTCTTTTCTCAGacaac                                             >  2:127975/1‑136 (MQ=255)

                                                                                 gAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCATTATTATTTCGTGTTGTCGGACAAGTGCCTGCTTTGCCATTATCGGTCGTCTCAGATACGtt                                           >  2:316605/1‑140 (MQ=255)

                                                                                 gAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGGTGTCGTCTCAGATACGtt                                           >  1:183553/1‑140 (MQ=255)

                                                                                   aTTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAg                                         >  1:202782/1‑140 (MQ=255)

                                                                                      gTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAggct                                      >  2:125934/1‑138 (MQ=255)

                                                                                        tattaGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCATAGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGt                                    >  2:131490/1‑140 (MQ=255)

                                                                                                     tttATCATTTGGATCGTCAGTTGGTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTg                       <  2:164279/140‑1 (MQ=255)

                                                                                                     tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGCAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCTGttttttact                       >  2:153154/1‑137 (MQ=255)

                                                                                                     tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATCCGTTAGGTTGTCCAGTCTTTTCTg                       >  2:316936/1‑140 (MQ=255)

                                                                                                     tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTATGTTGTCCAGTATTTTCTg                       >  1:183053/1‑140 (MQ=255)

                                                                                                     tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTACCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTATCTGTCGTCTCAGATACGTTCGCTTGTCCAGTATTTTCTg                       >  2:137894/1‑140 (MQ=255)

                                                                                                      ttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTCAGGTTGTCCAGTATTTTCTgg                      >  2:13983/1‑140 (MQ=255)

                                                                                                         tcttttGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgtgt                   <  1:264272/137‑1 (MQ=255)

                                                                                                         tCATTTGCATCATCAGTTGCTGATTTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgtgt                   <  1:151207/140‑1 (MQ=255)

                                                                                                             ttGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCTTCACTATTATTTGGTGTTGTCGGAGAAGCTTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCa               <  1:153156/140‑1 (MQ=255)

                                                                                                                 attatcaGTTGCTGATGTTACTGTTTTTTCACTTGTTGCCGCATCATTATTATTTGTTGTTGTCGGAGAAGTGTCTTCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAg           <  2:256610/137‑1 (MQ=255)

                                                                                                                 agtatcaGTTTCTGTTGTTATTGTTTTTTCACCTGTTGCCGCATCACCATTATTTGTTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTTTTGCATTAg           <  2:93072/137‑1 (MQ=255)

                                                                                                                  ttatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGc          <  1:135532/138‑1 (MQ=255)

                                                                                                                        gTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGa    >  2:166968/1‑140 (MQ=255)

                                                                                                                          tGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTCTTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAt  <  1:168193/140‑1 (MQ=255)

CCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAT  >  USA300TCH1516_ALE/2279573‑2279834

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