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 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,017,678	T→C	59.6%	F391S (TTC→TCC)	acp →	Sodium/proton‑dependent alanine carrier protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,017,678	0	T	C	59.6%	10.3 / 22.0	24	F391S (TTC→TCC)	acp	Sodium/proton‑dependent alanine carrier protein
Reads supporting (aligned to +/- strand): ref base T (4/5); new base C (5/9); total (9/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.29e-01

ATGCAACAGGTAAAGATTATTCAGGTACTGCGATGTATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACATTTTAC  >  USA300TCH1516_ALE/1017540‑1017817

aTGCAACAGGT‑AAGATTATTCAGGTACTGCGATGTATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTcttctt                                                                                                                                          <  1:142089/141‑1 (MQ=255)

              gATTATTCAGGTACTGCGATGTATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACa                                                                                                                             >  2:58493/1‑141 (MQ=255)

                   ttCAGGTACTGCGATGTATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAAtttt                                                                                                                        <  1:23444/141‑1 (MQ=255)

                   ttCAGGTACTGCGATGGATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAAtttt                                                                                                                        <  1:299174/141‑1 (MQ=255)

                       ggTACTGCGATGTATGCACGAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCg                                                                                                                    >  1:237205/1‑141 (MQ=255)

                             gCGATGTATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGtactac                                                                                                              <  2:39750/141‑1 (MQ=255)

                                    aTGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACACTTTTGTCGTCCTACTACATTa                                                                                                       >  1:35230/1‑141 (MQ=255)

                                                 cATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGt                                                                                          >  1:331799/1‑141 (MQ=255)

                                                 cATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGt                                                                                          <  1:369870/141‑1 (MQ=255)

                                                            ggTTCCTTGGTCGTGTTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACCAATGTTGCTTATTTaa                                                                               <  2:321480/140‑1 (MQ=255)

                                                            cGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTaa                                                                               <  1:39065/141‑1 (MQ=255)

                                                            cGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTaa                                                                               <  2:375050/141‑1 (MQ=255)

                                                                ccATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAAcgcg                                                                           >  2:17877/1‑141 (MQ=255)

                                                                 cATGGTAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGt                                                                          <  2:214915/141‑1 (MQ=255)

                                                                                    ttGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGttt                                                       >  2:101260/1‑141 (MQ=255)

                                                                                                 ctctGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGAtatttat                                          <  1:117282/141‑1 (MQ=255)

                                                                                                  tctGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGAtatttatt                                         <  1:101260/141‑1 (MQ=255)

                                                                                                          aGGTTCGTACTTTATTGCATTTGCTTTATTCTGCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGGTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGc                                 <  1:264304/141‑1 (MQ=255)

                                                                                                          aGGTTCGTACTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTAAACTTGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGc                                 <  1:271435/141‑1 (MQ=255)

                                                                                                                   cTTTATTGCATTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGAATTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGat                        <  1:74592/141‑1 (MQ=255)

                                                                                                                     ttATTTCATTTTCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGAACCACTACATTACAGAAACAAATGTTACTTATTTAACTCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGatta                      <  2:16040/141‑1 (MQ=255)

                                                                                                                     tgaTTGCATTTGCTTGATTCTCCTTTGCATTTACTATAATTTTGTCGTACTACTAAATTACACAAACAAATGTTGCTTATTTCACGCGTAATCAAAATAATCAAGTTTCATTGATATTTATTAATATTGCTCGTGTGatta                      <  2:29421/139‑1 (MQ=255)

                                                                                                                            aTTTGCTTTATTCTCCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGTCCGTGTGATTATTTTGtt               >  2:306955/1‑141 (MQ=255)

                                                                                                                                    tATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACAt       >  2:172608/1‑141 (MQ=255)

                                                                                                                                    tATTCTCCTTTGCATTTACTAAAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACAt       >  1:335304/1‑141 (MQ=255)

                                                                                                                                      ttctccTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACAttt     <  1:17877/141‑1 (MQ=255)

                                                                                                                                       tctcctGTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGTTTTTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACAtttt    <  1:13300/141‑1 (MQ=255)

                                                                                                                                         ttcttTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACATTTTAc  <  2:183090/141‑1 (MQ=255)

ATGCAACAGGTAAAGATTATTCAGGTACTGCGATGTATGCACAAGCCGGCATTGATAAAGCGTTCCATGGCAGTGGTTATCAATTTGATCCTACTTTCTCTGGCGTAGGTTCGTACTTTATTGCATTTGCTTTATTCTTCTTTGCATTTACTACAATTTTGTCGTACTACTACATTACAGAAACAAATGTTGCTTATTTAACGCGTAATCAAAATAATCAAGTTTCATCGATATTTATTAATATTGCTCGTGTGATTATTTTGTTCGCTACATTTTAC  >  USA300TCH1516_ALE/1017540‑1017817

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A