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
A5 F1 I1 R1	81	47.9	2225048	94.8%	2109345	113.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,504,515	C→T	R267C (CGC→TGC)	insQ →	IS609 transposase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,504,515	0	C	T	98.0%	171.8 / NA	51	R267C (CGC→TGC)	insQ	IS609 transposase B
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (23/27); minor base G (1/0); total (24/27)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATA  >  NC_000913/1504379‑1504644

tATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGgtgc                                                                                                                                 >  2:1080196/1‑139 (MQ=255)

     cAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGt                                                                                                                            >  2:321078/1‑139 (MQ=255)

            ccGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCa                                                                                                                     >  2:689942/1‑139 (MQ=255)

                aGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAAt                                                                                                                 <  2:96310/139‑1 (MQ=255)

                       aCCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAGTGATAGTCATTGAGGATTTGAAGGTCAGCAACATGACAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTACGCGCAAAATCAGGttt                                                                                                          >  2:683226/1‑139 (MQ=255)

                               aaaTTCACAACGGCC‑TTAGGCAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTc                                                                                                 <  1:823924/139‑1 (MQ=255)

                               aaaGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                  <  1:1080196/139‑1 (MQ=255)

                               aaaGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                  <  1:896251/139‑1 (MQ=255)

                               aaaGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                  <  1:1086382/139‑1 (MQ=255)

                                aaGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGgtgc                                                                                                                                 >  2:723010/1‑107 (MQ=255)

                                  gTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCa                                                                                                                                <  1:411253/106‑1 (MQ=255)

                                  gTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCa                                                                                                                                >  2:411253/1‑106 (MQ=255)

                                  gTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAAccatt                                                                                                  <  2:664795/136‑4 (MQ=255)

                                  gTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGa                                                                                               >  2:524725/1‑139 (MQ=255)

                                  gTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCAtt                                                                                                  >  1:664795/1‑136 (MQ=255)

                                     acaACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATAc                                                                                            <  1:689942/139‑1 (MQ=255)

                                     acaACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATAc                                                                                            <  1:847307/139‑1 (MQ=255)

                                      caACGGCCGTCAGCAAAAACCACGCAATGTTAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCa                                                                                                                     <  1:421699/113‑1 (MQ=255)

                                      caACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCa                                                                                                                     >  2:421699/1‑113 (MQ=255)

                                      caACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACt                                                                                           >  2:869131/1‑139 (MQ=255)

                                        aCGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTgg                                                                                         >  2:250302/1‑139 (MQ=255)

                                           gCCGTCAGCAAAAACCACCCAATGTTAGTCATGGAGGTTTTGAAGGTCACCAACATGTAAAGTTCGCCGGCGGTAAGGGTCAGCCAGCGGGGGGGCAAGTTCGGGGTAAAATAGGTTTTAAACGGTCCGAAACTgatcc                                                                                      >  2:823924/1‑135 (MQ=255)

                                               tCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                  <  2:190245/139‑1 (MQ=255)

                                               tCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                  <  1:259368/139‑1 (MQ=255)

                                               tCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                  <  1:42987/139‑1 (MQ=255)

                                                                   aTAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCgccgcc                                                              <  1:797632/139‑1 (MQ=255)

                                                                       tCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCt                                                          >  1:778471/1‑139 (MQ=255)

                                                                         aTTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTg                                                        >  2:276764/1‑139 (MQ=255)

                                                                           tGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                  <  2:841635/95‑1 (MQ=255)

                                                                           tGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                  >  1:841635/1‑95 (MQ=255)

                                                                           tGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATTCTGGATCAGGGCTGGTCTGAAATg                                                                     <  2:678248/124‑1 (MQ=255)

                                                                           tGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                  >  1:1110443/1‑111 (MQ=255)

                                                                           tGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                  <  2:1110443/111‑1 (MQ=255)

                                                                           tGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATg                                                                     >  1:678248/1‑124 (MQ=255)

                                                                                 tttGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAag                                                >  2:497996/1‑139 (MQ=255)

                                                                                                  tGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCgg                               >  2:1071645/1‑139 (MQ=255)

                                                                                                  tGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGAT‑AGGGGTGGTATGAAGTGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGt                              <  1:683226/139‑1 (MQ=255)

                                                                                                   gTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGt                              >  2:476692/1‑139 (MQ=255)

                                                                                                       aaGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAgg                          <  1:276764/139‑1 (MQ=255)

                                                                                                              cagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGc                                                                                 <  1:18489/77‑1 (MQ=255)

                                                                                                              cagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGc                                                                                 >  2:18489/1‑77 (MQ=255)

                                                                                                              cagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGtgcttgc                   >  2:565660/1‑139 (MQ=255)

                                                                                                                   ggTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTc              >  1:875012/1‑139 (MQ=255)

                                                                                                                     tACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCg            <  1:476692/139‑1 (MQ=255)

                                                                                                                     tACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCg            <  2:778471/139‑1 (MQ=255)

                                                                                                                     tACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCg            <  1:913265/139‑1 (MQ=255)

                                                                                                                      aCGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGc           <  1:321078/139‑1 (MQ=255)

                                                                                                                          tCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGc       <  2:875012/139‑1 (MQ=255)

                                                                                                                           cagccagcCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCg      >  1:1079519/1‑139 (MQ=255)

                                                                                                                              ccagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATAc                                                                                            >  1:630320/1‑50 (MQ=255)

                                                                                                                              ccagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATAc                                                                                            <  2:630320/50‑1 (MQ=255)

                                                                                                                              ccagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGtat   >  2:634687/1‑139 (MQ=255)

                                                                                                                               cagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGtata  <  1:250302/139‑1 (MQ=255)

TATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATA  >  NC_000913/1504379‑1504644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A