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
A7 F67 I0 R1	54	74.6	1619566	95.7%	1549924	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,440,085	G→T	100%	intergenic (‑45/‑891)	cspA ← / → xpaC	cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,440,085	0	G	T	98.0%	122.2 / ‑5.5	42	intergenic (‑45/‑891)	cspA/xpaC	cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (24/17); minor base A (0/1); total (24/18)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA  >  CP000730/1439947‑1440221

cTGAAAATTGTACGAATACGTCATTTTTTCCTTCAACTTCGATACACCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTAACTTGTTTCATAATCTGAAACATCCAAGACTAAAATTCATTCAAAATCCTTATTCTCa                                                                                                                                        >  2:158079/1‑141 (MQ=255)

cTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCCCCAAGACTAAAATTCATTCAATATGCTTATTCTCa                                                                                                                                        >  2:331819/1‑141 (MQ=255)

          tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa                                                                                                                              <  1:499625/141‑1 (MQ=255)

          tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa                                                                                                                              >  1:316247/1‑141 (MQ=255)

          tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTATTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa                                                                                                                              >  1:544669/1‑141 (MQ=255)

            cGAATATGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaaa                                                                                                                            >  2:212941/1‑141 (MQ=255)

                    tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCa                                                                                                                    >  2:166638/1‑141 (MQ=255)

                     cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCaa                                                                                                                   <  2:311254/141‑1 (MQ=255)

                           ctcCTTCAACTTCGATAAAGCCGAATCCTTTTTTTTTTTTTTTTTTTTTAAATGTACATTGTTTCATAATCTTTACCTTCCAAGAGTTAAAATCATTCATAATGCTTATTCTTATATTTCTATATCTACATTCTAATTTCa                                                                                                             >  2:414465/1‑141 (MQ=255)

                           ctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGAAAATTTCa                                                                                                             >  2:222875/1‑141 (MQ=255)

                           ctcCTTCAAATTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATCCTCATATTACAAAAAATCCATGCACAttccc                                                                                                             >  2:612097/1‑138 (MQ=255)

                               ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCa                                                                                                         <  2:766738/141‑1 (MQ=255)

                               ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCa                                                                                                         <  2:348815/141‑1 (MQ=255)

                                       cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCACATATTCt                                                                                                 >  1:404536/1‑141 (MQ=255)

                                         aTAAAGCCTAATCCTTTTTCAGCGTGAAGCCATTTAACTGAACCCTCTTTCATAATCTCAAGCCTCCAAAATTAAAATTCATTCAATATTCTTATTAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCttt                                                                                               <  2:574837/141‑1 (MQ=255)

                                                     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                                                   <  2:659224/141‑1 (MQ=255)

                                                     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                                                   <  1:166638/141‑1 (MQ=255)

                                                        ttttCAGCCTTCAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat                                                                                <  1:249048/141‑1 (MQ=255)

                                                                   aaaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTaa                                                                     <  1:212941/141‑1 (MQ=255)

                                                                     aCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAAATCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATGTCGCTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACt                                                                   <  2:592378/141‑1 (MQ=255)

                                                                          ttAACTTTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                                              <  2:70964/141‑1 (MQ=255)

                                                                           tAACTTTACTTTGGTTCATAATCTGAAACCTCCAAGACTACAACTCACACCATCAACTTTTTCTCTTACTATAAAATATACATGCAATTGTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatt                                                             <  2:487516/141‑1 (MQ=255)

                                                                             aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCCATATGGAGTGATCATCTGCTTAATTTGtattat                                                           >  1:235056/1‑141 (MQ=255)

                                                                             aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                           >  1:557820/1‑141 (MQ=255)

                                                                                      tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATATTGCAGtt                                                  >  2:11090/1‑141 (MQ=255)

                                                                                      tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                                  >  2:787599/1‑141 (MQ=255)

                                                                                      tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                                  >  1:51833/1‑141 (MQ=255)

                                                                                         ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                               <  2:221096/141‑1 (MQ=255)

                                                                                         ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                               <  2:323530/141‑1 (MQ=255)

                                                                                               atgtgaccaaacccaGACCAAAATTCATTCAATATACTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAAAATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCaaa                                         >  2:376874/15‑141 (MQ=255)

                                                                                               aTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATCCATGCAAATTTCACTTAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATCGTTCAGTTATTACCaca                                         >  2:450549/1‑139 (MQ=255)

                                                                                                       ccTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaata                                 >  1:605913/1‑141 (MQ=255)

                                                                                                            aaGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaata                            >  1:637428/1‑141 (MQ=255)

                                                                                                              gACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTTTTATATTGCAGTTATTACCAAATTTCAATACaataat                          >  2:265363/1‑141 (MQ=255)

                                                                                                                    aaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaacaaa                    >  1:70738/1‑141 (MQ=255)

                                                                                                                          ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa              <  1:353934/141‑1 (MQ=255)

                                                                                                                          ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa              <  1:424900/141‑1 (MQ=255)

                                                                                                                             aaTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGACTAATCATCTGCTTAACTTGTATTATAGTTCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCAttt           >  1:62299/1‑141 (MQ=255)

                                                                                                                                  gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATCCAATAATAAAAAATATTCATTTAAACa      >  2:13829/1‑141 (MQ=255)

                                                                                                                                  gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCa      >  1:125034/1‑141 (MQ=255)

                                                                                                                                    ttATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAat    <  1:687398/141‑1 (MQ=255)

                                                                                                                                      aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta  <  2:605913/141‑1 (MQ=255)

CTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA  >  CP000730/1439947‑1440221

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