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
A2 F28 I1 R1	116	98.7	3298914	99.2%	3272522	139.9

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	96.5%	101.1 / ‑2.6	29	intergenic (‑77/+180)	iraM/ymgK	anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK
Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (17/11); total (18/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.73e-01

CTGAAAAAGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTA‑‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTT  >  NC_000913/1211946‑1212202

cTGAAAAAGATATACCAAATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTA‑‑ccccc                                                                                                                        >  2:1545210/1‑140 (MQ=255)

 tGAAAAAGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTA‑‑cccccc                                                                                                                       >  1:426992/1‑140 (MQ=255)

     aaaGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTA‑‑cccccccccc                                                                                                                   >  1:1198577/1‑138 (MQ=255)

                 caTGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAaaat‑aaa                                                                                                       <  2:1366537/140‑1 (MQ=255)

                             aTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAatg                                                                                           <  2:514390/140‑1 (MQ=255)

                             aTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAatg                                                                                           <  2:106829/140‑1 (MQ=255)

                             aTTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAatg                                                                                           <  2:496488/140‑1 (MQ=255)

                              ttACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTACCCCCCCCCCTCAAAAAAAT‑AAATTAATTAAAatg                                                                                           <  2:1198577/140‑1 (MQ=255)

                              ttACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAatga                                                                                          >  2:223163/1‑140 (MQ=255)

                                               aTCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATataaaataa                                                                         >  1:74337/1‑140 (MQ=255)

                                                    cTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTACCCCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGCTTTATATAAAATAAAAtt                                                                     >  2:1150064/1‑140 (MQ=255)

                                                     ttCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTa                                                                   >  1:1156156/1‑140 (MQ=255)

                                                          ttGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCa                                                              <  1:940923/140‑1 (MQ=255)

                                                          ttGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCa                                                              <  2:824051/140‑1 (MQ=255)

                                                               aTGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGaa                                                         <  1:223163/140‑1 (MQ=255)

                                                                     tATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCaa                                                   >  1:231797/1‑140 (MQ=255)

                                                                      aTCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAAt                                                  <  2:497009/140‑1 (MQ=255)

                                                                       tCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATg                                                 >  1:1129120/1‑140 (MQ=255)

                                                                        cccACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATgg                                                <  2:1177428/140‑1 (MQ=255)

                                                                            cGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGt                                            >  2:10905/1‑140 (MQ=255)

                                                                                 tttAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAAc                                       >  2:1039437/1‑140 (MQ=255)

                                                                                         ggTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCCAAAAAATAAAATAAATAAAAATGTTGCTTTAT‑TAAAAAAAAAGTTAAAAGAAAGAAATTCCATGGGTTTTAAAAAAAATtag                               >  2:1306236/1‑140 (MQ=255)

                                                                                         ggTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCCCAAAAAAAA‑AAAATAATTAAAATGGTGGGTTTTATAAAAAAAAATTTAAAGCAAGGAAACTCAAAGGGTTTTTAAAAAAATgaa                               >  2:591621/1‑139 (MQ=255)

                                                                                           ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTACCCCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATgaga                              >  1:887480/1‑140 (MQ=255)

                                                                                           ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGAt                             >  2:1246779/1‑140 (MQ=255)

                                                                                           ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTA‑‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGAtt                            >  1:480894/1‑140 (MQ=255)

                                                                                                     tGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAg                   >  2:1388512/1‑140 (MQ=255)

                                                                                                     tGTTTATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAg                   <  1:1330234/140‑1 (MQ=255)

                                                                                                       tttATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCa                 >  2:999598/1‑140 (MQ=255)

                                                                                                         tATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAAt               >  2:1005848/1‑140 (MQ=255)

                                                                                                         tATTTCTTGATTTTGCATATGAGTATATTAC‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAAt               >  1:1054929/1‑140 (MQ=255)

                                                                                                                      tGCATATGAGTATATTAC‑CCCCCCCCCCAAAAAAAT‑AAATTAATTAAAATGATGGGTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACtt  >  2:642491/1‑140 (MQ=255)

CTGAAAAAGATATACCACATGTAGGTTGAATTACCGTGTCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATTA‑‑CCCCCCCCTCAAAAAAAT‑AAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTT  >  NC_000913/1211946‑1212202

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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