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
A3 F18 I1 R1	9	30.2	693202	94.8%	657155	140.9

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	97.5%	111.6 / NA	40	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (15/24); minor base T (0/1); total (15/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGC  >  USA300TCH1516_ALE/2279570‑2279838

gtgCCGTTATTAGTTGGTTCTACTGCTGGTTTACTAGTTACAGCGTTATCCATTGTCTGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtgtt                                                                                                                                   <  2:169706/141‑1 (MQ=255)

 tgCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTAATGAATCTACTCTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtgctt                                                                                                                                  >  2:209910/1‑138 (MQ=255)

  tccGTTTTTCGTTGTTTCTTCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATTTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtgtt‑gt                                                                                                                                <  2:185528/140‑1 (MQ=255)

             ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTg                                                                                                                     <  1:346309/141‑1 (MQ=255)

             ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTg                                                                                                                     <  2:178625/141‑1 (MQ=255)

                aTTCTAGTTCGGGTTTACTAGTTACATCGTTACCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCg                                                                                                                  <  1:27543/141‑1 (MQ=255)

                aTTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCg                                                                                                                  <  1:111565/141‑1 (MQ=255)

                      cTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACCCTCGTTGTCTTATTAGCTCGTGGTGGACTATTTGCATCATCAGTTGCTGAGGTTACTGTT‑GTTTCACCTGTTGCTGCATCAc                                                                                                            >  2:246175/1‑141 (MQ=255)

                      cTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCAc                                                                                                            <  1:321319/141‑1 (MQ=255)

                        tCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACtt                                                                                                          >  2:14698/1‑140 (MQ=255)

                        tCTGGTGTAGTAGTTACATCGTTATCCTTTGTCGGCCTGTTTGTTGATGCTTCTACAGTAGAATTGTCATTAGCTTGCGGTTTATCTTTTGCATCATCAGTTGCTGTTATTACTGTT‑GTTTCACCTGTTGCCGCATCACta                                                                                                          <  2:305828/141‑1 (MQ=255)

                          tGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGCT‑GTTTCACCTGTTGCCGCATCACtatt                                                                                                        >  1:18406/1‑141 (MQ=255)

                             tttACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACTTGTTGCCGCATCACTattatt                                                                                                     >  2:312635/1‑141 (MQ=255)

                                 ttAGTTACATCGTTATCCTTTGTCGGACTGTTTGTTTATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGgt                                                                                                 <  2:128109/140‑1 (MQ=255)

                                 gtAGTTATATTGTTTTTTATTGTGGGACTGTTTGTTGATGGATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGgt                                                                                                 <  2:333850/140‑1 (MQ=255)

                                 cTAGTTACATCGTTATCCAGTGTAGGATTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGgt                                                                                                 <  2:129755/141‑1 (MQ=255)

                                            gTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCCCTATTATTTGGTGTTGTCGgaga                                                                                      >  1:338568/1‑141 (MQ=255)

                                             ttATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGaa                                                                                     >  1:259523/1‑141 (MQ=255)

                                             ttATCCATTGTCGGACAGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGgagca                                                                                     >  1:310992/1‑139 (MQ=255)

                                                      gTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCt                                                                            <  1:110271/141‑1 (MQ=255)

                                                      gTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTCTATCACCCTGAGCATCAGTTGTTGCTGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCt                                                                            <  2:336416/141‑1 (MQ=255)

                                                           aCTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGcc                                                                       >  1:197882/1‑141 (MQ=255)

                                                                 ttttgATGCATCTACACTAGAATTGTGTTTATCTTGCGGTTTCTCATTTGCATCATCAGTTGCTGATGTTAATGTTCGTGTC‑CGTGTTGGTTTAACGCTATTATTTGGTGTCGTCGGAGAAGCGTTTGCTTTGCCATTAGc                                                                 <  2:74698/139‑1 (MQ=255)

                                                                 tgttgATGCTTCTACATTAGAATTGTTATTAGCTTTCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc                                                                 <  2:152173/141‑1 (MQ=255)

                                                                         cATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGtct                                                         <  2:197882/141‑1 (MQ=255)

                                                                              acacTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGAt                                                    >  1:286448/1‑141 (MQ=255)

                                                                                    gAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTCCCATTAGCTGTCGTCCCAGATACCttt                                              >  2:64808/1‑140 (MQ=255)

                                                                                              taGCTTGCTGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg                                    <  1:51022/141‑1 (MQ=255)

                                                                                              taGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg                                    <  1:105864/141‑1 (MQ=255)

                                                                                                        tttATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTTGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTgt                          >  2:267067/1‑140 (MQ=255)

                                                                                                         ttATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgt                         <  1:302618/141‑1 (MQ=255)

                                                                                                         ttATCATTTGCATCATCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgt                         <  1:73602/141‑1 (MQ=255)

                                                                                                               tttGCATCAGCAGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCGGGATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCa                   <  2:338568/141‑1 (MQ=255)

                                                                                                                       atcaGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAgaaaa           >  2:223964/1‑137 (MQ=255)

                                                                                                                        tcaGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAttt          >  1:84008/1‑141 (MQ=255)

                                                                                                                         caGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTA‑TTTCTGGTGTTGCATTAGCATTTGa        <  2:342793/141‑1 (MQ=255)

                                                                                                                          aGTTGCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGa        <  1:223964/141‑1 (MQ=255)

                                                                                                                              gCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAttt    <  1:340498/141‑1 (MQ=255)

                                                                                                                              gCTGATGTTACTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGAGTTGTCGGAGAAGCGTCTGCTTTGCCATTAACTATTTTCACAAATACATTAGGTTGTCCAATATATTCTGGTGTTGCATTATCATTTGAAttt    >  2:227967/1‑141 (MQ=255)

                                                                                                                                tGATGTGTCTGTT‑GTTTGACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGc  <  2:128343/141‑1 (MQ=255)

GTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTT‑GTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGC  >  USA300TCH1516_ALE/2279570‑2279838

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