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 F28 I1 R1	161	50.8	1735388	98.6%	1711092	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,212,088	(C)_8→9	intergenic (‑85/+172)	iraM ← / ← ymgK	anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,212,080	1	.	C	86.7%	86.4 / 7.7	30	intergenic (‑77/+180)	iraM/ymgK	anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK
Reads supporting (aligned to +/- strand): ref base . (2/2); new base C (16/10); total (18/12)
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

TGAAAAAGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATT  >  NC_000913/1211947‑1212197

tGAAAAAGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑cccccc                                                                                                                 >  2:37022/1‑140 (MQ=255)

   aaaaGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑ccccccccc                                                                                                              >  1:476301/1‑139 (MQ=255)

   aaaaGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑ccccccccc                                                                                                              >  2:295806/1‑139 (MQ=255)

    aaaGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑ccccccccct                                                                                                             >  2:133522/1‑138 (MQ=255)

         tataCCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCaaaa                                                                                                         >  1:844401/1‑140 (MQ=255)

                      ggTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAaattaatt                                                                                            >  2:147106/1‑140 (MQ=255)

                           aaTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAat                                                                                       >  1:258890/1‑140 (MQ=255)

                           aaTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAat                                                                                       >  1:50248/1‑140 (MQ=255)

                           aaTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAat                                                                                       >  2:241723/1‑140 (MQ=255)

                            aTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTTC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                      <  2:661681/140‑1 (MQ=255)

                            aTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                      <  2:606709/140‑1 (MQ=255)

                                               tCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATataaaataaa                                                                   >  2:685937/1‑140 (MQ=255)

                                               tCCACTTCATTTGTTATGTCTTATCCCAC‑GTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATAtaaaataaaa                                                                  >  1:151968/1‑140 (MQ=255)

                                                       aTTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAga                                                          >  2:364224/1‑139 (MQ=255)

                                                           gTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAg                                                       <  2:844401/140‑1 (MQ=255)

                                                               tGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAAt                                                   <  2:246761/140‑1 (MQ=255)

                                                                     aTCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAAt                                             <  1:133522/140‑1 (MQ=255)

                                                                     aTCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAAt                                             <  2:50248/140‑1 (MQ=255)

                                                                     aTCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCCCAAt                                             <  1:295806/140‑1 (MQ=255)

                                                                           cGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGt                                       >  2:586304/1‑140 (MQ=255)

                                                                           cGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGt                                       >  1:447545/1‑140 (MQ=255)

                                                                           cGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGt                                       >  1:831113/1‑140 (MQ=255)

                                                                                         gTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATgaga                         <  2:258890/140‑1 (MQ=255)

                                                                                          ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGAt                        >  2:349952/1‑140 (MQ=255)

                                                                                          ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGAt                        >  2:773630/1‑140 (MQ=255)

                                                                                          ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGAt                        >  2:814865/1‑140 (MQ=255)

                                                                                          ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGAt                        >  2:835917/1‑140 (MQ=255)

                                                                                               tAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTtgt                   >  1:528336/1‑140 (MQ=255)

                                                                                               tAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTtgt                   >  2:681676/1‑140 (MQ=255)

                                                                                                   aTGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAg              <  2:720831/140‑1 (MQ=255)

                                                                                                    tGTTTATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAg              <  1:685937/140‑1 (MQ=255)

                                                                                                      tttATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCa            <  1:586304/140‑1 (MQ=255)

                                                                                                        tATTTCTTGATTTTGCATATGAGTATA‑TTACCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAAt          <  1:37022/140‑1 (MQ=255)

                                                                                                               tGATTTTGCATATGAGTATA‑TTA‑CCCCCCCCCTAAAAAAATAAATTAATTAAAATTTTGGGTTATTAAAAATAAAATTTAAAGCAAGGAATTTCAATGGATTTTAAAAAAAATGGAATTTTTTGAAAGCAATAAattatt  >  2:472640/1‑140 (MQ=255)

TGAAAAAGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATA‑TTA‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATT  >  NC_000913/1211947‑1212197

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A