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
A21 F42 I0 R1	24	30.6	687070	95.0%	652716	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,373,697:1	+T	20.0%	coding (79/1335 nt)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,373,697	1	.	T	20.0%	59.9 / 16.2	25	coding (79/1335 nt)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base . (8/12); new base T (2/3); total (10/15)
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

TGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAAC  >  USA300TCH1516_ALE/2373559‑2373835

tGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTGAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑Ta                                                                                                                                          >  2:197627/1‑141 (MQ=255)

tGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑tt                                                                                                                                          <  1:74134/141‑2 (MQ=255)

       cGAGCCTACGAATGCTGCTAATGCAGTCGTGACAAAAATGGCATCTTGGTCCATTTTCATATCATCTGATACGCCTTGAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGt                                                                                                                                   <  2:276683/141‑1 (MQ=255)

         cgCCTACAGATGCTGCTAATGCAGTCGCTACAAAACTGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTtg                                                                                                                                 <  2:221752/140‑1 (MQ=255)

                        ctAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAg                                                                                                                   >  1:107046/1‑141 (MQ=255)

                         tAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGa                                                                                                                  <  2:269778/141‑1 (MQ=255)

                            tGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTtc                                                                                                              <  1:75813/141‑1 (MQ=255)

                                   tcTACAAACATGGTACCTTGGTTCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAGAGTTGTGATACCGCCTAAGATTTCTCTTTTa                                                                                                       <  2:109262/140‑1 (MQ=255)

                                    cTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGCTTTCTCTTTTaa                                                                                                      >  1:111827/1‑141 (MQ=255)

                                       cAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAg                                                                                                    >  2:324528/1‑141 (MQ=255)

                                           aaTGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGt                                                                                               <  1:321048/141‑1 (MQ=255)

                                            aTGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTGAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGtt                                                                                              <  1:197627/141‑1 (MQ=255)

                                                                cATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCAATAGA‑TAAGAAAGTTGTGATACCACATAAGATTTCTATTTTAAAGTTTGTTTCATATTTATCGAACttgta                                                                          >  2:316253/1‑137 (MQ=255)

                                                                        ctGAGACGCCTGTAACATCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGtttt                                                                  <  1:159146/141‑1 (MQ=255)

                                                                              cGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTACGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAATTTTTCACGa                                                            >  1:82/1‑141 (MQ=255)

                                                                               gCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGTCTAAGATTTCTCTTTTAAAGTTTGTTTCATATTTATCGAACTGAAAATAGTTTTTCACGaa                                                           >  2:178711/1‑141 (MQ=255)

                                                                                    tAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGGTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCTATATTTATCGAACTGGAAATAGTTTTTTGCGTATggtt                                                      >  1:61128/1‑139 (MQ=255)

                                                                                            gCTAAACTTAAAACGTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttt                                              <  1:27252/141‑1 (MQ=255)

                                                                                             cTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGATTAAAAACATGGGGGTACCGCCTAAGATTTTTCGTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttt                                              <  1:324528/141‑1 (MQ=255)

                                                                                              tAAACTTAAGACCTGCAGGTTGACTGCTAAAATATAGGCCATAGA‑TAAGAGAGTGGTGATACCGGCTAAGATTTCTCTTTGAGAGTTTGTGCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttttt                                            <  2:343316/141‑1 (MQ=255)

                                                                                              tAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttttt                                            <  1:123214/141‑1 (MQ=255)

                                                                                              tAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCttttt                                            <  1:114158/141‑1 (MQ=255)

                                                                                                            gCGGGCTAACTGCTAAAATATAGGCCATAGATTAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTa                               <  1:226229/141‑1 (MQ=255)

                                                                                                             cGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCGAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAAt                             <  1:119221/141‑1 (MQ=255)

                                                                                                                       gCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAatat                   >  1:218027/1‑141 (MQ=255)

                                                                                                                                        aGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTTTTTTTTTTTTATAGTTTAATATCATTCTTAATATAAAAc  >  2:231455/1‑141 (MQ=255)

TGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTTAAAACTTGCGGGTTAACTGCTAAAATATAGGCCATAGA‑TAAGAAAGTTGTGATACCGCCTAAGATTTCTCTTTTAAAGTTTGTTCCATATTTATCGAACTGGAAATAGTTTTTCACGAATGGATGCTCCTTTTTTTAAAATACCTTAATAGTTTAATATCATTCTTAATAAAAAAC  >  USA300TCH1516_ALE/2373559‑2373835

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